FCP- compressor to blu-ray- I end up with a ton of extra chapters!

I have a 2 hour (1:55) 1080p29.97 pro-res timeline (and media) that I have exported to self contained movie with Chapter Markers selected. I imported to Compressor and the correct amount of chapter markers showed up. I then used the presets (although lowered bit-rate to 26 average and set for multi-pass) for blu-ray and used the end action to create a blu-ray. All looks great except I ended up with about 10 extra chapters about 2/3 the way in the movie, they are unnamed on the menu screen. Plus, I have one that has a time at about 3-hours (which is of course far outside of the movie length).
This all after a 48-hour encode in compressor. I checked my sequece in Final Cut and it only has the chapter markers I intended, and they all are named. Any ideas on where to look for what might be causing this? I wish I could just edit the .img file to remove the unwanted chapters, but am not finding a solution for that either.
I am using the latest Leopard (not Snow Leopard) and the latest version of FCS.
Message was edited by: mpetrucco to correct typos

OK. Up until C4.0, Qmaster was a stand-alone application and accessible through the Preference Pane in Systems Preferences. In C4.0, and until 4.0.7, it became an embedded app – found within the Compressor.app file. That's why you don't ordinarily encounter the Qmaster file…you have to go digging to find it. (And it's altogether different in 4.1) 
Russ

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