Did you try uninstalling VD before and install it AFTER CCCP that second time?
this is interesting as that had said they fixed this. as in their release notes in the most recent version (2006-03-06) they say this
If you still want your Virtual Dub (I'm not sure why but that not for me to decide) once you install it AFTER CCCP. Follow this to make it work with Xvid filesFinally added the VfW part of ffdshow (after much complaining from people who wanted to do stuff in VirtualDub)
XviD in VirtualDub
If all else there is always VirtualDubMod that has support for the matroska container format.
anyways thats all for now report back if you have anything else