Though it is possible that malware or large number's of DLL files in these folders could cause the extremely slow scans, it isn't the only cause.
Over the last couple weeks we've been seeing a number of these apparent hangs or freezes, usually starting with the CoolWWWSearch detections though also occasionally in other later detections.
The only confirmed issue found at this point is an interaction with the Yahoo AntiSpyware program, which was confirmed by removing that program and scanning again. There was also another case which appeared to be caused by a different and less well known program. In either case, running the scan in Safe Mode seemed to work fine, which pointed to a probable interaction with other loaded software that wasn't loading in Safe Mode.
I noticed that you had mentioned some kind of issue running a scan in Safe Mode, but I don't really understand what the problem was. If you could confirm that the scan works in Safe Mode and let us know what other anti-malware programs you are running we might possibly be able to help.