It’s funny, I came across this post because we have been having a very similar problem since we upgraded to fcp7. We make these 1:00 spots where the footage is shot XDCAM 24p, ultimately converting it to SD 29.97 and mixing it with various SD graphics, film clips, etc.
In fcp 6 we would make an XDCAM 24p seq, edit in that (so no rendering) and then when done, we’d copy and paste into a 29.97 sequence. (This is only to then set graphics and make approval QTs; for the final 24 to 29.97 we run the footage through a Terranex or something) In fcp6 this copy and paste presented no problem. A few flash frames, as the op mentioned…
But now in 7 it seems the way fcp makes the conversion is completely different. It drops some shots altogether, moves video and audio all over the map…
We managed to find a workaround by exporting an xml of the fcp7 HD sequence, importing into a machine we have that’s running fcp6, doing the copy & paste there, and then reopening that into 7.
It’s a pretty specific scenario, so I haven’t really found much else online about this problem…for us, it’s actually making it worth keeping one machine on fcp6…