The first thing I think you need to do is to find out what corrupt files exist that SFC couldn't repair. The following website gives an easy method to use to find out which files are bad:
http://www.dummies.com/how-to/content/how-to-find-what-files-sfc-could-not-repair.html
If your CBS log file is huge, you might want to rename the CBS.log file to CBS.bak, then run SFC /scannow again from an elevated command prompt to recreate the log without all the extra junk to make it easier to search.
Post back the names of the corrupt files. There was a bad Windows update last month that cause file corruption problems for some folks. Until I finally figured it out and managed to fix it, I was getting random file system corruption, slow operation, and boot failures on my system (got to the point where I even did a repair install, which lasted until the next Windows update when Micro$oft reinstalled the bad update).