2006 HHR sounds goes in and out of right and rear speakers...

Chevrolet HHR Car Radio Wiring Chart Car Radio Battery Constant 12v+ Wire: Red/White
Car Radio Accessory Switched 12v+ Wire: Run a wire to the steering column and use the brown wire at the front of the center console on the passenger side.
Car Radio Ground Wire: Black/White
Car Stereo Power Antenna Trigger Wire: Pink
Car Stereo Amp Turn On Trigger Wire: Pink Left Front Speaker Positive Wire (+): Tan
Left Front Speaker Negative Wire (-): Dark Green
Right Front Speaker Positive Wire (+): Light Green/White
Right Front Speaker Negative Wire (-): Light Green
Left Rear Speaker Positive Wire (+): Brown
Left Rear Speaker Negative Wire (-): Brown/White
Right Rear Speaker Positive Wire (+): Dark Blue
Right Rear Speaker Negative Wire (-): Tan

all speakers r connected to the same wires on the radio
If left/right balance and front/rear fader work properly
and sound is coming out it is likely (but not definite) radio is ok and speaker wiring is the issue.
HOWEVER, if it sounds the same on both left and right, it could be the radio. It is unlikely both sides have the same issue at the same time without it being in the radio.
The only way to verify it to disconnect the speaker and substitute a known good speaker.
So back to troubleshooting.

Sounds like a wire is shorting out, probably in behind the stereo, but more likely in the back where the speakers connect. Check for something shorting out or a wire grounding out near the speaker.
You can trace back from there.
Other than that probably is the stereo.

Not hooked up properly..maybe just loose wires

The Amp in the trunk might have blown,
Town Car Radio Wire Diagram
Car Radio Battery Constant 12v+ Wire: Pink/Light Blue
Car Radio Accessory Switched 12v+ Wire: Yellow/Black
Car Radio Ground Wire: Black/Light Green
Car Radio Illumination Wire: Light Blue/Red
Car Stereo Dimmer Wire: Blue/Red
Car Stereo Antenna Trigger Wire: Blue
Car Stereo Amplifier Location: Trunk
Car Audio Front Speakers Size: 5? x 7? Speakers
Car Audio Front Speakers Location: Doors
Left Front Speaker Positive Wire (+): Orange/Light Green
Left Front Speaker Negative Wire (-): Light Blue/White
Right Front Speaker Positive Wire (+): White/Light Green
Right Front Speaker Negative Wire (-): Dark Green/Orange
Car Audio Rear Speakers Size: 6? x 9? Speakers[img src="http://www.assoc-amazon.com/e/ir?t=modilife-20&l=as2&o=1&a=B00009UHRE" width="1" height="1" border="0" alt="">
Car Audio Rear Speakers Location: Rear Deck
Left Rear Speaker Positive Wire (+): Gray/Light Blue
Left Rear Speaker Negative Wire (-): Tan/Yellow
Right Rear Speaker Positive Wire (+): Orange/Red
Right Rear Speaker Negative Wire (-): Brown/Pink
Check the fuses

The most common solution is both rear speakers are bad. Not what you expect, but is what we usually find. could be a driver in the radio.
Go back to the rear speaker and put your ear right on the speaker and notice if there is a faint sound.
Have a test speaker and plug up before you buy the correct ones.

I have the same problem mine is 2007 model what could be causing this?

Sounds like a loose ground. Obtain a good volt/ohm meter and the wiring shop manual for your model and trace out the wires.
You should be able to find and fix the problem.
Sometimes weather will wrinkle the cones in speakers. Check yours, if they are dried and distorted take them to the parts counter guy and get new ones.

maybe the balance control is turned all the way to the right.

if this does not work:
a speaker wire is broken most likely where it enters the unit.

I would remove the radio and test the speaker leads for appropriate resistance (probably 4 ohms per speaker)

DOES THE RADIO PLAY? HERE ARE THE FACTORY WIRING COLORS FOR THE RADIO HARNESS, RECHECK YOUR WORK. IF U FIND NOTHING THEN IF THE RADIO PLAYS THE CD PLAYER IS DEFECTIVE, IT HAPPENS BELIEVE ME.

2001 Chrysler 300M Car Stereo Wiring Diagram
Car Radio Battery Constant 12v+ Wire: Pink
Car Radio Accessory Switched 12v+ Wire: Red/White
Car Radio Ground Wire: Chassis or Strap
Car Radio Illumination Wire: N/A
Car Stereo Dimmer Wire: Orange
Car Stereo Antenna Trigger Wire: Orange/Red
Car Stereo Cell Phone Mute Wire: N/A
Car Stereo Amp Trigger Wire: N/A
Car Stereo Amplifier Location: Located under the rear deck in the trunk.
Car Audio Front Speakers Size: N/A
Car Audio Front Speakers Location: N/A
Left Front Speaker Positive Wire (+): Dark Green
Left Front Speaker Negative Wire (-): Brown/Red
Right Front Speaker Positive Wire (+): Violet
Right Front Speaker Negative Wire (-): Dark Blue/Red
Car Audio Rear Speakers Size: N/A
Car Audio Rear Speakers Location: N/A
Left Rear Speaker Positive Wire (+): Brown/Yellow
Left Rear Speaker Negative Wire (-): Brown/Light Blue
Right Rear Speaker Positive Wire (+): Dark Blue/White
Right Rear Speaker Negative Wire (-): Dark Blue/Orange