The drivers for the graphics card have separate corrections for normal desktop and video playback (at least nvidia). Check settings on the nvidia control panel or in CCC for Radeon. Perhaps reïnstall driver.
Reïnstall codecs; most programs use the same codec, so changing programs doesn't always solve an issue. Maybe try third party codec pack (free). Have a look at the playback settings of the programs to see if there are alternative playback methods and try those.
Maybe the video hardware acceleration on the card is going south, but that's just a wild guess, not even sure that's possible.
Just throwing some thoughts out there.
