I can create a new custom preflight profile, but when I apply it to a document, InDesign freezes.
I've tried various documents.
I tried just adding minor checks to the preflight profile, but still with no luck.
CS6 on OSX 10.8
It's not happening to me when I create a custom profile in InDesign CS6. I'm running Mac OS X 10.7.4.
I note that you appear to be using prerelease Mountain Lion OS X software (10.8). Perhaps there is a conflict between beta OS X software and InDesign.
It turns out that it's a font problem. I couldn't get a corrupted font that was specced out of the file. i couldn't save to IDML, export the story or much of anything else. I had to rebuild the file.