I have a new rule of thumb regarding HDV. It goes like this:
If you capture HDV from tape, always transcode into Cineform codec AVIs. There are just too many formatting problems to work with the native m2t clips that were aquired from the tape.
If you shoot the HDV tapeless with either a DR-60 or the compact flash unit that comes with the Z7 or s270, go ahead and use the native m2t clips. They will work just fine.