Right click the CCCleaner program and select "Run as Administrator" and that might solve your problem with it not letting you clean files. Alternatively, boot into safe mode and then do it from there.
To check if it is a problematic program, use the msconfig.exe program (just type msconfig in the search bar of the start menu) and then choose selective startup. Go into the "Startup" tab and uncheck everything (unless this is a laptop, then you want to double check each startup program so that the basic device software such as keyboard and monitor etc are loading) and then save setting and restart. Load up sound recorder (again, just type into startup) and test your mic from there. If it works in that configuration, your issue is an installed program, which I would then go through the list and load stuff one at a time to see where the problem lies, starting with audio programs such as teamspeak, mumble, iTunes, etc.
Since you don't think you did anything crazy after it worked during the raid and then the next day it didn't, do you have auto-updates for Windows and other programs turned on? If so, and it might be painful, but go into the update manager (Windows Update, for example) and look at the update history and see if anything was updated during the time frame. Then just roll back those specific changes and see if that fixes the issue. It isn't super uncommon for a hotfix that solves one problem to break something else by accident.
