M1V R11 Joy stick blinks 5 times

Contact Invacare direct. I can't find anything on Charger Blink Codes, only for the scooters.

Invacare® Pegasus

Invacare http://invacare.ca > doc_files
4) Wait two seconds until the appropriate blink code is displayed on the battery charge display, then release the keys. Do not hold the keystroke combination ...
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Throw away

The diagnostic code would indicate a bad control box. It could also be too low a voltage from the batteries or a bad or broken wire or connector between the joystick and the control box. Chair will need a technician from a good dealer to help out if battery's and wiring are good.

The M51 could have the motor clutch levers in the free wheel/push mode and the joystick will not blink if this is the case. Make sure that the chair cannot be pushed. If it can be pushed it means it is in free wheel and you need to lock the motors in gear.

If it is in gear and the joysticks green light does not change color or blink it could be that the joystick is bad. When nothing happens and the lights don't blink when you push the joystick knob the chairs controller basically isn't recognizing the joystick movement.
Time to have the joystick repaired or more. Have a technician look at it.

5 blinks means the brake has a problem
http://manuals.monsterscooterparts.com/mobility/Invacare/manual-invacare-lynx-L3-L4.pdf

It is indicating a left motor fault, which is not good news. This is usually from a motor overheating and burning out, usually from overloading the chair or from driving it on unstable terrain like mud, snow, wet grass or sand. If that is the case, there could be more damage to the electronics once you get the motor replaced too. Replacing the motor is a lot of work and very expensive, so you may want to try to find a replacement chair.

Here's your M51 manual:
http://www.invacare.com/doc_files/1125085J.pdf
Trouble codes start at p25.
Also, Invacare is proud of the M51's wet-weather performance (check the "Rain Test" chapter in the manual. You might have a warranty issue. Check with an Invacare dealer.

Ranch well the red flash indicates a low battery and the 5 flashes indicate a bad left brake. Now try charging the batteries until you get a green light on your charger then turn on the chair it shouldn't flash the red if the batteries are accepting the charge. If your batteries are 2-3 years old it could be time to change them. If Medicare paid for your chair then they will pay most of the repair costs. You can contact your provider for help or a service company like Roadrunner Mobility @ 1-800-467-2668 or Repair Xpress @ 1-877-581-3733. If Medicare did buy the chair then you are eligible for a new chair every 5 years and yours is almost 8 years old. Contact a local provider that you trust to check into getting you a new chair. Hope this helps you