Suddenly bad FCP exports...is it the codec?

Hi everyone. I'm on a work G5, so the specs below do not apply to the system I am on right now.
FCP is updated to 5.1.4 on here.
I've been making regular FCP exports everyday and as "Current Settings" and unselected "Make Movie Self-Contained". One day it just gives me bad exports to where the beginning and end are normal, but the middle is bad. It looks like it's stuck on a few frames and flashes. Is this the codec? Either way, any advice?
Thank you!

Hard to tell what's going on without seeing the footage.  Progressive footage will have a slightly jerkier (is that a word?) look than interlaced footage particularly in horizontal movement.  That may be what's happening. 
Make sure that your field dominance is set to none through out your workflow.  
Also, how are you monitoring in fcp?  If you're viewing on a video monitor via a card like the aja or blackmagic, and you're not seeing the problem, then there's probably something wrong in your export process. 
If you have a short shot you can send me in the original format where the problem is noticeable I'll take a quck look.  My email is in my profile.

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