Hello,
I had the same trouble a while ago, but I managed to sort it out.
Instead of exporting a SWF from flash, export a 720 x 576 25fps quicktime movie (if working with PAL), or NTSC equivilant. Then create a new project in FCP, go to the sequence menu and then Settings, change it from DV to Animation.
Bingo!
Your sorted!
Dave