Windows 7: Not sure if CHKDSK stuck or should wait it out.

Ok so my computer was not booting up so last night I went to the built in startup repair in Windows 7 and through the command prompt did a "chkdsk c: /f /b" which I saw online. It took about 15 hrs to get where it is at now which it finished the stage 5 and now says "Free space verification is complete." I thought that meant it finished but im assuming not because it won't let me type in the CMD box. Its been at this point for about 2 hours now and im wondering if I should try to shut down and boot up my computer or wait out until it does more. Also during stage 4 it said a couple times that windows repaired bad clusters.

Sounds like your hard drive is in trouble. I'd shut it down then run the hard drive manufacturers diagnostic to see if it finds any problems.