The Rockman Anime Music Video Station

Pretty much, do what KF and Gemini said. But f it continues, you could be using massive effects at one time, or on the same clip, causing WMM to fail. I had this problem once, and I got rid of the effect and it worked fine. Usually, splitting a clip and adding 2x speed or 2x slower speed then goin to the next clip and adding the opposite ( 2x speed =/= 2x slower ) will cause WMM to do this as well.

Thanks you lot, I'll try out what you guys said and see if it works.

EDIT:
Im currently in the making of a Hellsing AMV and for once the clips "seem" to go with the music, does that help a little bit?

WMM likes to fool you... usually it doesn't show flashes of other clips until you've saved it as a WMV, so be prepared to constantly tweak it...

Also it likes to make it seem as if clips go with something when they don't... that's happened twice to me.