Keeps hanging up saying there are duplicate files, then stalling out

Compressor will compress my video all the way to half way, then red exclamation marks will appear next to the two files saying that there are duplicate files with the same name... to preserve the original files change the name of the file I'm compressing. So I change the name, and then the progress line stalls out forever like it gets stuck after it tells me to change the name.

Actually, this sounds like normal behavior.
When you click the submit button, Compressor passes the encoding job to QMaster. QMaster then starts writing the necessary files in the destination that you set with the filename that you set.
Compressor sees the new files being written into your destination, and puts up the alert. This is standard behavior. There is no need to change the output filename in Compressor once the job has been submitted.
Compressor doesn't need to be kept open once you submit the job. To monitor the encoding, open Batch Monitor.

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