What version of Compressor are you using? We frequently compress batches up to 50 or more regularly without problem. We export both out of FCP directly or from dropping QT's in from Finder. Additionally, we used compressor 2 for a long time and now on our 8-cores with Compressor 3 and things have gotten much much faster, tho i sincerely hate the new interface.
So, it seems like you need an update or reinstall because obviously Compressor isn't working as it should. There is a 3.1 update you should have, since your going to ProRes
You do realize also that this is going to take a long long time, as this is a difficult transcode. Do you really need ProRes? FCP 6 can handle multi-formats pretty well now, especially on a 8-core. Perhaps just change your sequence render settings to ProRes to get some better performance...