System file corrupted? FCP and quicktime suddenly can't convert AVIs

Yesterday I could open an 12 minute AVI file in quick time, go to "Save As" and save it as a MOV file, which would take about 45 seconds, as far as i can see it's a rewrap, not a conversion, but tell me if i'm wrong.
Ive been trying to find the best way to do this on batch, so i've been trying to do do it using Final Cut Pro's batch export tool (ran very slow, crashed a couple of times) and MPEG Streamclip's batch tool (which worked fine, and speedy, but files came out looking interlaced). But finding out how to do this in batches isn't my problem at the moment.
The problem is that today, all the programs seem to struggle with the conversion. What would have taken 45 seconds in quicktime yesterday seems to take up to an hour today. MPEG streamclip suffers similar slow down issues. Final Cut Pro can't even start converting today.
I was just wondering what could have changed to make this happen to all 3 programs at once. I'm assuming that it's a codec, or something that they all reference in the conversion process. I dont know what that would be or where it would be, or how to fix it. If any one could shed any light on any part of this I would be eternally grateful.
The files are dv pal avis, standard definition. Ive tried re-installing Quicktime, I put in the final cut pro disc to see if there was a repair option but there wasnt one. final cut version 6.0.6, quicktime 7.6.4, streamclip 1.9.2
Message was edited by: aceswild
Message was edited by: aceswild

Are any of the PDFs set to PDF/A already or have security set. I don't think either are allowed when doing the combine function.

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