FLAC (
http://en.wikipedia.org/wiki/FLAC) is an audio codec and shouldn't have an effect on your video playback. I'd be surprised if this is the culprit.
You could almost rule out Windows Media Video 9 as it is from Microsoft and should be thoroughly tested by their engineers, but there is always the chance.
More likely, it may be a result of some codec pack you downloaded and installed. Possibly from a conflict between an old ffdshow and DivX and/or XviD. These reports are unconfirmed.
Some possibly helpful links:
http://support.microsoft.com/kb/269967
http://www.divxmovies.com/faq/#4.8
I'd uninstall any codec pack I can find and then re-install the stuff you really need. I suggest the latest CCCP (link in my signature), XviD (for encoding AMVs - optional), then any other codec you find you really need (FLAC, OGG, etc.), although most can be decoded by ffdshow.
You could also try updating your video drivers.