I’m in the same boat…or worse because my project it’s longer and it takes “minutes”!!! just clicking on items not even change settings or other…really strange.
It happened to me also…after upgraded to FCP Studio, Compressor became unreliable at all…lately it took 47hrs to compress 9 min DV… randomly pixels and artifacts.
Look in ~/Library/Application Support/Compressor folder if you still have Compressor 1.x preset trash the whole folder.
Then relaunch Compressor it will recreate the folder with the new preset only…old preset doesn’t work in Compressor 2, as Apple state at this page: