i'm not quite sure what kind of files those are, but your best bet would probably be to take the files into quicktime and export them with a new codec that final cut likes...most likely the DV/DVCPRO NTSC codec (or PAL if you use PAL).
if not that, i'd say take them into Compressor and save them as the same codec i mentioned above.
other than that I dont know what to tell you, but even though final cut can be a picky bastard at times, he will have the tools to fix the things you want fixed =)