The only reason that it should have been faster using Virtualdub is if you were using different settings. Encoding time is dependant upon resolution, bitrate, number of passes, etc. If you changed any of these settings between using one program and using the other then you'll get different results.
Oh, and I voted for XviD. Free, and nearly as good as other payware codecs. Plus it's very configurable and editable, unlike wmv.