VDubMod can't handle MKVs with ISO formatted MPEG-4 (and by that I mean *both* Advanced Simple Profile - i.e. DivX and XviD - and H.264). And VFW-mode H.264 is borked - the forward ref problem is something that commonly happens with VFW-mode H.264.
In addition, VirtualDub and VDubMod use VFW; those files not working anymore is due to a lack of a VFW decoder (DirectShowSource will only work if you've got a DirectShow decoder, meaning that if you can't play the video in Windows Media Player it won't work either). If you had recently removed all your video codecs or simply had a fresh install of the OS and only cared to put in the CCCP, then you don't have a VFW decoder (although from others' reports the CCCP now doesn't strip out ffdshow's VFW interface, but I've no way to test that - all I know is that it definitely used to do so, making it editor-unfriendly).
If you've got ffdshow, go into its VFW configuration (may also be labeled as 'video encoder configuration' on some builds) and on the 'Decoder' tab, select 'libavcodec' for those formats that need decoding. If that doesn't handle it, you're out of luck. If you need the
full version of ffdshow (or if you're in need of a
recent build; by recent, I mean a version from the past six months), then look here:
http://sourceforge.net/project/showfile ... _id=173941
Instead of DirectShowSource, you could try FFmpegSource:
http://forum.doom9.org/showthread.php?t=127037