What are the odds - I ran into the same scenario with a WMV after I posted my comment
I think I have it figured out though (at least this solution worked for me). It looks like depending on how the WMV is encoded, payback gets cut.
I took my "bad" WMV file and ran it through Windows Movie Maker Live (the version that comes with Windows 7). Basically all it did was take my "bad" WMV and save it as a different WMV file. My best guess as to why this worked was that the two different WMV files used different CODECs. A WMV file can be encoded in WMV1, WMV2, or WMV3. My source file that didn't work was WMV2, the one that was reencoded was WMV3.
Hope that helps.