Brightness fluctuations on mkv's

All my movies/tv shows are stored on another PC that is always on and i use my htpc to play the files over the network.

Since these files are downloaded from the web I would chalk it up to bad encodes but the same "bad" file would play fine when streamed using ps3 media server and my ps3 instead of using my htpc

I also have Live TV on my htpc and ive never seen it happen there. i use the netflix and hulu wmc app and all is fine there also.

i use the i3 igpu, lav filters and mediabrowser for all my mkv's.

What could be causing this on certain files. I have the igpu and wmc refresh rate set to 59, could that be it? my tv is a panny vt25 and my htpc runs through my pioneer 1021 AVR using hdmi

Any advice?

Thanks for the reply, i will try this out and report back. Even though my problem does not occur during live tv its worth a shot.