My key starts the car but the locks will not activate using the fob buttons and the indicators no longer flash even when i use the key to lock the car

google how to program fob for 2011 chevy malibu for more info

On the Chevy key fob, press and hold the "Unlock" and "Lock" buttons at the same time until you hear the door lock and unlock again. This means you're all set. Re-insert the programmed key back into the ignition to the "On" position to finish the Chevy key fob programming process

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CODE ALARM SYSTEM
information is always subject to change and correction Used on:
Impreza 1996-2001
Legacy 1995-1999
Forester 1998-2000
Battery GP-23A
Lock: Left button will lock all doors. Double chirp indicates locked.
Unlock: Right button will unlock driver's door only. Hold unlock button app 6 seconds, it will unlock all doors including rear gate. Single chirp indicated unlock.
If the car chirps or lights flash 4x the alarm was triggered.
Panic. Press both buttons to activate emergency honk and flashing lights.
Valet mode: With optional alarm only Press the red alarm button on the left of the steering wheel. The light will quickly double flash. To re-set back to normal mode, press the red alarm light button again

Battery failed and lights flashing?
Parking lights will flash when the vehicle's battery is disconnected and reconnected.
To stop lights from flashing, either:
Press remote transmitter “UNLOCK” button once OR turn the ignition switch to the “ON” position and press programming button for one second (see below).
The vehicle interior (courtesy) light and door open warning light (DOOR AJAR indicator) will then illuminate for 60 seconds when the ignition is turned off, or until the doors are locked with the remote transmitter. Yes, the dashboard instrument panel lights will flash when the parking lights flash.
Programming or Overriding the Alarm when you have lost the remote
Open driver's door.
Turn ignition key to 'On'
Press and *hold programming button* in (see diagram, button under dashboard)
After 15 seconds the the door locks will cycle 3 times. Do not release Programming button
Press lock (left) button the remotes to be programmed. The door locks will cycle one time.
Exit programming mode by releasing Programming button under dashboard and turning key to off.

Code Alarm Programming Button is under dashboard on the kick panel by the driver's left knee, left of the steering column. If you can't find it, it might still be tucked up in the wiring harness higher up in that same general area. The botton is recessed in a plastic ring (see diagram).
This button must be pressed while programming remotes or if the battery was disconnected and the lights are flashing.
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I don't know about turning the alarm system off completely, but if you are trying to get it to stop chirping the horn and flashing the lights when locking/unlocking the doors, I found the following in the Ram 3500 Owner's Manual:

To lock the doors: Press and release the LOCK button on the transmitter to lock all doors. If the ignition is OFF, when the doors are locked, the parking lights will flash on once and the horn will chirp once.

The horn chirp feature will be shipped from the assembly plants activated. If desired this feature can be disabled by using the following procedure:
1. Perform this operation while standing outside the vehicle.
2. Press and hold the LOCK button on a programmed (i.e. functional) key fob.
3. Continue to hold the LOCK button, wait at least 4 seconds, but no longer than 10 seconds, then press and hold the PANIC button. Release both buttons at the same time.
4. To reactivate this feature, repeat the above steps.

Vehicles will be shipped from the assembly plants with the park lamp flash feature activated. If desired, this feature can be disabled by using the following procedure:
1. Perform this operation while standing outside the vehicle.
2. Press and hold the UNLOCK button on a programmed (i.e. functional) key fob.
3. Continue to hold the UNLOCK button, wait at least 4 seconds, but no longer than 10 seconds, then press and hold the LOCK button. Release both buttons at the same time.
4. To reactivate this feature, repeat the above steps.

There is a possibility that your key fob might lost the programming. I suggest that you re-program your key fob, follow the next steps to re-program it.

Instructions

1. • 1 Sit in the vehicle and close all the doors. Insert the key into the ignition.
     
   • 2 Turn the key to the "Off" position then to the "On" position. Repeat this until the door locks cycle to indicate that the programming mode is activated. End with the ignition key in the "On" position.
     
   • 3 Press the "Unlock" or "Lock" button on the programmable remote. Listen for the doors to lock or unlock to verify successful programming.
     
   • 4 Turn the ignition key to the "Off" position. Listen for the door locks to cycle to indicate that you have exited the programming mode.
     
   • 5 Repeat the above steps to add any additional remotes.
     

Read more : http://www.ehow.com/how_7446180_program-key-fob-kia-optima.html

You are going to have to use the Key fob or remote alarm fob to go threw a set of lock and unlock procedure. Crank the car shut it off remove the key outside the vehicle at a distance of at least 30ft then lock the car, wait till it arms and the dash light blinks once this is active you want to unlock the car with the remote. If this one does not work do the same thing except when you unlock it do so with the key to re open after arming security.Also make sure you have both fobs or all remote fobs with you when you do this lock with one unlock with the other then vise, versa ok if you need any further help just ask also make sure your battery is fully charged and the terminals are clean this will affect a security system bad a low battery or low battery in the FOB's.

The alarm system needs to be de-activated by turning the key to the unlock position at the drivers door lock cylinder when re-connecting the battery. The alarm control module cannot be disconnected otherwise the vehicle will not start.

First thing, does the red light on the remote light up when you push any of the button
if no, then replace battery inside remote
if yes, then try repograming the remote to the car again.
-Have both remote ready. fob#1 and fob#2 (doesn't matter which one is #1 or #2)
-each step has to be done within 5 sec or it will not work, but don't do it super fast.
1.turn key just to the "on" position (not starting) and push "lock button " on fob#1 once and release
2.turn key off
3.turn key just to the "on" position (not starting)and push "lock button " on fob#1 once and release
4.turn key off
5.turn key just to the "on" position (not starting)and push "lock button " on fob#1 once and release
6turn key off
7.turn key just to the "on" position (not starting) and push "lock button " on fob#1 twice (if you only have one fob, then stop here and go to step 7)and push the "lock button" on fob#2 twice.
8.turn key off and remove key from ignition.
if you did it right, remotes should work again.
good luck

should not be using fob buttons for entry or locking for emergency only .if keyless entry walk up to car with fob do not press any buttons see if door opens then walk away from car with fob about 20m then go back to car without fob and see if door locked if so all working fine .indicators will not flash if the above dont work take back to main dealer for diagnostics keys may need to be reprogrammed

Insert key into door barrel or ignition lock and turn key, whilst doing this press the unlock/lock button, the led on the dash should flash to indicate this has initialised the key to the car, then remove key and test operation of remote. If this fails then a new remote plus coding to the car by your dealership is needed

You should not have to reset the key fob after a battery replacement. The signal from the key fob stays the same and is programed to the reciever.
If the key fob needs to be reprogrammed then follow these steps.
1. Have all key fobs with you during programming.
2. Sit in the vehicle with all doors closed.
3. Lock all doors using the Lock/Unlock switch on the door.
4. Insert and withdraw the ignition key 7 to 9 times within 10 seconds (do not turn the key, just insert and withdraw).
5. The 4 way flasher indicator on the dash should flash once or twice.
6. Insert the ignition key and turn it on (key on, engine off).
7. Press any button on one remote and the 4 way flasher indicator on the dash should flash once.
8. If you have more key fobs to program use the Lock/Unlock button on the door to unlock the doors and then lock the doors.
9. Press any button on the next key fob and the 4 way flasher indicator on the dash should flash once.
10. Repeat if you have more key fobs. Only 5 can be programmed.
11. To exit, simply turn of the igniton and remove the ignition key.
12. Unlock the doors using the Lock/Unlock switch on the door and exit the vehicle.
13. Make sure the window is down when testing remotes in case you leave the keys inside.
14. Close all doors and test all remotes that were programmed.

Do not skip any steps or the process will not work.

If the 4 way flasher indicator does not work when inserting the key, you will need to start the process from the begining. If it still does not work the receiver may be your problem.

If the 4 way flasher indicator does not flash when pressing any button on the key fob then the key fob is the problem (dead battery or defective remote)