Odd. Never seen that happen, never heard of it happening.
But I don't put it in Program Files anymore, preferring to create C:\Portable\ and then putting non-installing apps in there. Sometimes post-XP Windows getting pissy when stuff is put into PF.
The "filters" are technically plugins, so look in the plugins folders. Move all of those somewhre else. I'd put back 5 at a time, relaunch
VirtualDub. 5 more, repeat.
Yes, there are multiple plugins folders (_/32/64) and you can ignore the "removed" folders.
A most likely issue is your computer is missing a common dependency needed by one of the filters.