Getting choppy footage when rendering plus "flash" frames

Hi all,
I've been using Final Cut Pro 7 for about two years for casual video editing. I use H.264 files with a framerate of 24fps and I always set sequences to fit the native format of the video files I use in them. Today, I noticed an odd "bug" when rendering video files. It's a bit hard to explain, but I'll try my best.
Let's say I take a 5-second clip from an hour-long video file and place it in the timeline. I cut off a bit of the end and add some keyframes to adjust the opacity. I then render this small piece. However, upon playback, the footage appears to "stagger", and even the playhead appears to pause for a moment before continuing on. This is confusing to me, because the footage is rendered properly, so shouldn't it play normally, like the unedited segment of the clip?
I've also had a problem with getting "flashes" of a frame that isn't meant to be in said clip. When I scroll over the clip using the playhead, this "flashing" frame is nowhere to be found.
I'm using Mountain Lion (10.8.5).
Can anyone lend a hand with this? Thanks in advance.

David and Ian are absolutely correct in their posts about the problems with trying to work with h264 quicktimes in fcp. But the issues you are having may also have something to do with your frame rate.
Do you mean 24 fps or 24P? 24p is actually 23.976 frames per second. Most US video is 29.97 fps and 23.976 fps is a relatively easy conversion to 29.97 fps using "pulldown." Early DSLR's sometimes shot exactly 24 or 30 frames per second. New DSLR's now shoot 23.976 and 29.97. Unfortunately, spec sheets don't always describe the frame rate accurately. 24 fps is not a standard video frame rate and there can be problems putting a 24 fps clip in a 24p sequence.
Here's a user tip describing these frame rate issues in greater detail
https://discussions.apple.com/docs/DOC-4731
If any of this isn't clear, post back. It's complicated.

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Thank you for your reply - over the past few days I have been able to
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806.791.6329
From:   Chinmay Baid <[email protected]>
To:     Daniel Spray <[email protected]>
Date:   03/03/2011 05:09 AM
Subject:        Why do I get "Publish
Failed" when I select F4V with fixed frame rate?
Hi,
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http://blogs.adobe.com/captivate

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