Enable 'motors' in the logs (http://code.google.com/p/arducopter/wiki/AC2_datalog), then you can see the output to each motor. Feel the temperature of each ESC when the problem occurs. Also check if the problem occurs when there are only a few sats found by the GPS or when in the flight.
Will enable it in the logs.
I'm flying without gps at the moment.
I have an intermittent problem where the left rear motor's power decreases suddenly but recovers if I throttle down, land and take off again, but it only seems to happen if the GPS has not got a 3D lock yet. I'd be interested to know if you're having something similar.
I'm also flying X and it seems to be the left aft motor thats giving me the problem.
The GPS is installed again and as soon the weather permits I'll test.
Yesterday it crashed due to the power/thrust loss into a hedge.
Just flew a battery with GPS installed and motor problem is gone.
Could this be a SW issue?