Blocky Sorenson 3 exports from FCP5

I'm exporting fairly long (40-60 min) QTs for a P.A. to transcribe. I'm using Sorenson 3 compression, and re-sizing to 320x240, to keep disk space low. My original files are DV with no additonal compression.
The start of my exported files look great, and then somewhere in the middle they become EXTREMELY blocky with tons of artifacts. On some files, the image is crisp again at the end.
Motion JPEG-A compression DOES work -- it held its look throughout the whole hour-long file.
I've trashed all my old QT 6 and 7 receipts from the Library, and have re-installed QT 7.1 fresh -- still no luck. The only receipts I haven't thrown out seem to be for either MPEG or Pro functionality, and I don't want to pay $30 for an upgrade I already have.
Does anyone know why my FCP or Mac would have trouble exporting long QTs with Sorenson 3 compression, but not with Motion JPEG-A compression?
Thanks.

Skydo, I saw your questions over at the FCP discussion yesterday. And they thought you would get a better answer to your question here.
As for me I've never liked Sorenson 3. I think you said you had the quality slider halfway. But never mention what key frame setting or bit rate your using.
Slider being half way and a high setting for key frames with a low bit rate will give you a bad compression.
I've had great success with H.264 out of FPC. Some people hate compressor, being slow. But with both FCP/Compressor I can fine tune my compression to were you can't tell the H.264 from the original. I all way use one pass first, being fast. If it looks great I use it. If not I go for the multi-pass. Thus adding more compression time. You can add compression and edit makers at places in the video were you think you'll have compression problems.
There a ton of things you can use in FCP/Compressor to make great video that people over look.

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