H.264/MPEG-4 AVC footage problems

I am using footage from a Canon 5D Markiii, on an iMac with an external firewire drive. I have been having problems with exporting the video. More specifically, the footage looks fine on the timeline (in FCP 7) and when it is exported, the video now has several pixelated frames and missing frames. Is this an issue with H.264/MPEG-4 AVC footage? Is there another video format that I could convert this footage into that would work without these output glitches?

You mention FCP7 but you post in the FCPX forum, so I assume you are having these issues in FCPX. Here are a few suggestions:
Import your H264/AVCHD footage as prores 422. This makes a larger but more efficient file for your NLE to work with.
If you're using FCPX, make sure that if you imported PROXY footage, you are not exporting proxy footage. That's a low resolution copy of the footage that requires less power for editing but when outputting, unless you want low resolution draft footage to review, it needs to be changed back. That preference would need to be changed back to "Original or Optimized footage".
The issue is not specifically with H264 or AVCHD footage, but rather how you are processing it, or perhaps an applied effect that may be causing the issue. More specs on your computer hardware and software versions would be helpful.

I am very sorry. I thought I was on the FCP 7 forum. My mistake.

No probs, it has been moved