I have a similar problem with CTM 2.8.155286.178 in Win7 x64. After I installed CTM, Windows booting has becoming a bit of a lottery. Sometimes it goes through, but sometimes gets hanged before the initial display, with the underscore DOS-like cursor parked at the top left corner or with a blank display. If so, the machine needs to be cold booted to respond again. Upon cold booting, and after the CTM display, Windows brings up the notice its previous booting had failed and gives the option of either "fixing" the system files or continue as normal. Except in one occasion I was able to continue without trouble; in such occasion, selecting to continue rebooted the machine and brought back the same notice. Because I would only resort to MS fixes as the very, very last option (i.e., using the MS fix or setting myself alight bonzo style), I decided to loose whatever had added to the machine since the last CTM snapshot, and restored the system to that time to escape this MS-fix loop.
It is an inconvenience, of course, but unless it gets worse I am still willing to keep CTM. There are no usual suspects as far as I can tell. This is a very lean Win7 machine. Any suggestions from Comodo on how to avoid this nuisance?