Try rolling back your FCP to 5.1.4 and see if the problem goes away. If so, then obviously, something has been changed in the project settings to cause your problem.
We use DVCAMs/DV decks all day long and we’re NOT seeing anything other than normal interlacing with 6.0.
Upgrading software mid project is never a good idea… and now you know why. Has anything else changed in your monitoring chain? Different monitor? Cables? Monitoring cards (Kona, BM, etc.).
If the only thing that’s different is FCP 6.0, then go deep into the project settings to see what’s different.
Good luck.
mark