By "choppy" do you mean processor lag/ computer trying to catch up, missing frames, or maybe a "strobing" effect?
Can you give some details about the computer (processor, ram, video card,etc)? Was your footage shot 24p?
Perhaps a dumb question, but are you viewing your footage on the FCP canvas or on a reference monitor?
If you haven't already, you should do a test print-to-video and see if the footage looks "choppy".
If this is a post problem, you may find some better answers on a different forum like DvInfo.net or creativecow.
Best of luck.