Another good choice to convert with, if you don't want to deal with the time-engulfing issues that surround MPEG Streamclip and Visual Hub, is to get eyeTV 3. You can open the MPEG (both elementary and separated streams are compatible), then export to DV (easiest edit format for FCE4, IMHO)...
Cheers!
I'm wondering if adding the MPEG-2 Playback component would solve the issue.