What version of iPhoto are you using? I think Apple used to offer more options for photo-movie exporting, but it appears there is only one option with iPhoto5. That is MPEG-4 exporting, which should be fine for FCP. In earlier versions, the default was a Photo-JPEG non-video Image Sequence. Since this is not technically video, QT could not export it correctly to other video codecs. What you would need to do is go to the advanced export options and export a movie that is video. Since I don’t have a previous version of iPhoto installed anymore, I can’t explain it step-by-step.
For instance, using the share movie option with iPhoto5, when opened in QT, the movie indicates that it is a MPEG-4 movie. With earlier versions and the default export settings, QT indicates it is Photo-JPEG with whatever effects (ie Cross Fade) are applied.