Well, the reason I asked about version and fresh install was because if you go back and read posts about bizarre issues, they are usually tied to upgrading to snow leopard or FCP7 verses doing a fresh install. From what I’ve read (and experienced) when going from version 6.5.whatever, to v7 you should do a fresh install of the software. Again, same with OS upgrades.
I suggested compressor, because it may help lead you down the path of finding out if it’s your source file, or a program error with Episode.
Could you look at your export from FCP and see if the issue is there? Or does it only show up after transcode?
-Jason