You "re-encoded" to MOV? With What codec... since "MOV" or "MP4" is just the container.
It is impossible to edit h.264 files reliably on FCP. So make sure you are using ProRes or some other codec that keeps the native resolution.
In your particular case, if it is not h.264 that is causing the problem, and if FCP handles other files with no problems, then look again how you are transcoding with MPEG-Streamclip. Maybe you have created an exotic mix of frame-sizes/bit/frame-rates?
If you are talking about AVCHD files, you know that your should use the log-and-transfer tool, or the software tool Sony provides for its cameras?
It was not me complaining about YouTube. I simply had a problem after initially installing FCP 7, and that was related to the Sound-configuration/kext.
good luck,
ninetto