Perian can cause problems. Temporarily uninstall it in System Preferences.
Mixing media the way you're doing and cause serious problems in media not being recognized. This appears in most camera manuals somewhere.
Trying shooting a short section on a new card in one format. Every manufacturer uses a different code for their different formats like HDFX, HDFH, HDHQ, HDLP. You have to tell us which one you're using and what format that selection uses. It will be in the camera manual.
You need to use FCE4.0.1 and set the correct format for the media you're using, one of the AVCHD formats that matches what you shot. You should be aware that FCE does not support 1080p24, 1080p60, or 1080p50. So do not shoot in one of those formats.