Okay, I got it to work for me.
Open QuickTime Player
Go to:
QuickTime Player Menu > QuickTime Preferences > Advanced
Check the box to "Show legacy encoders".
Right underneath the check box it says, "Allows exporting using older codecs"
I opened Compressor, nothing happened. Then restarted and opened compressor, and the boxes in compressor returned.
Then it occurred to me what might have made the boxes go away:
I initially set up my FCP import codec setting to : HDV 1080i.
But, I recently had to import an older, lower quality DV, which was shot 3 years ago. I had to change the codec setting to regular DV in order to import the video.
After I edited the DV video, I tried to push it to Compressor, and that was when I noticed that the Compressor Boxes were missing for the first time.
After I checked the Quicktime Box to "Show legacy encoders" (Allow exporting using older codecs). The boxes came back.
Not saying it will work for you, but I tried everything else: including 2 complete un-installations and re-installations, messing with Display settings and Expose, downloading Pacifist... and nothing worked for me.