I tested the problem in original (not altered) distros Mint9 and Mint10.
On both distros recordMyDesktop works fine.
Both video and audio are recording well.
Problems appears with Firefox (v3.6.x) plug-in Moonlight (v2 ).
The problem is with video recording, as the audio works fine.
If even a fragment of moonlight display area is present from
the beginning in the capture area, all capture is black.
If capture area is originally moonlight-free, all is best,
but if moonlight trans-passes later the recording area,
the resulting record is black where the moonlight invaded,
while rest of the recording area remains fine.
I tested Istanbul to similar result.
To test, go to: http://videolectures.net/gpip06_mackay_gpb/
chose: Switch to WM Player (as the default is Flash)
Wait for the stream to accumulate. Record.
Any suggestion where to begin?