5d mark II audio issue, firmware?

kinda sounds like a bad on-camera mic. But reply is right, the on-camera mic is only good for recording audio that you can sync with an external recorder's track.

I own several Rode mics and plugging them directly into camera isn't great. The 5Dmk2 has Automatic Gain Which is bad.

If you want to record in camera get a JuicedLink the new Riggy RA333 is great. You can also install Magic Lantern, but you wouldn't get the pre-amp boost to the mic.