My apologies for digging up an older thread, but I have noticed one thing when shooting video with my 5D Mark III and then editing on a Mac/FCP.
At work, all of my video editing is done on a Mac and FCP 7. Normally, I use a Sony HXR-NX5U, which FCP logs and transfers just fine. I'm aware that DSLR footage isn't native to FCP7 and as such, must be transcoded to ProRes for efficient editing. If I can't transcode directly via FCP, I use MPEG Streamclip.
With that said, I recently shot some footage on my 5D3 @ 1080p/24fps/ALL-I. I loaded the footage into MPEG Streamclip (latest build)....and the program promptly crashed. I tried again and got to the export screen, but it crashed again. I then loaded up FCP7 and entered the Log/Transfer menu, to transcode the ALL-I footage to ProRes. Same thing happened-- FCP crashed when trying to bring up the ALL-I footage.
So I went out and reshot the clips, this time in IPB. I brought the 5D3 IPB footage back to my Mac, loaded up MPEG Streamclip and voila: Footage was converted to ProRes MOV files without issue or crashing.
Now, I may be completely oblivious to some work around, or I may be having a "Master of the Obvious" moment, but for FCP/Mac users, I would advise shooting IPB to avoid transcoding headaches.
Of course, if you use Adobe Premiere 5.0/higher (as I do at home on my PC), then all this is bypassed, due to Premiere's native DSLR capabilities .
You might consider upgrading to the newer FCPX...it handles the files either way just fine.
I've had no problems with it using FCPX so far...no crashing, and you don't have to bother transcoding if you don't want to....