Convert VfW-codec based video to "normal" (Windows)
While it can't go direct to H.264, VirtualDub I believe can work with Vfw codecs and can transcode to something more compatible with your other tools.  I don't know if Quicktime for Windows supports Vfw codecs or not, but I do believe the Pro version of Quicktime supports H.264 encoding.  

If you have Adobe Media Encoder, it would also easily do what you are looking for, but I believe it only comes with the Adobe suite, thus would be prohibitively expensive if you don't have it already.