I'm not completely sure that this was the cause, but the last few days I when I have opened the Creation Kit and loaded up the Skyrim.esm, done something simple like adding a few statics to a cell, and then tried to save, the CK hung on the save window prompt. Today I was trying to think of possible causes since google search and forum search yielded nothing close to what I was getting, and the only thing I could think of was turning off the 'Sky' lighting. So I turned it off, and bam, it worked. There was a whole day between the last time I tried to save anything and today, so I don't know, something could have been updated, I didn't do too much digging to check.
I'm running Windows 7.
Anyway, if this is a known issue then ignore me. If not, I hope I can help someone having the same problem.