I selected all my audio files (3376) and tried Analyze Audio to see if I had missed any. Sure enough it said there were 58 files that needed to be done. I made sure Skip Analyzed Files was checked and then clicked Analyze. The progress bar started but the "0/58 completed" on the right didn't change. It then suddenly jumped to 58 completed but there were still Queued up files in the list.
I clicked Analyze again and this time the progress bar, "0/58 completed", and the Queue/Progress display box worked as expected. I stopped the analyze to see if I could reproduce it, but this time after a long, long wait and only the progress bar moving, everything started working as expected.
After it said completed even though the last file showed only 99%, there was still a long, long wait (like 5-10 minutes) before it actually finished so I could do anything else. It seems like it really can't figure out how to skip analyzed files as this should be a quick process.