In addition to those files you mentioned, your anti-virus will also scan your registry which accounts for many of the items scanned total.
Try doing your scans in "SAFE MODE
The Windows operating system protects files when they are being accessed by an application or a program. Malware writers create programs that can insert itself and hide in these protected areas when the files are being used. Using Safe Mode reduces the number of modules requesting files to only the essentials to make your computer functional. This in turn reduces the number of hiding places for malware, making it easier to find and delete the offending files. Using anti-malware tools, Scandisk, Chkdsk, Defrag, & Disk Cleanup in Safe Mode also speeds up the scanning process.
If your computer seems to be slow, read Slow Computer/Browser? Check here first; it may not be malware
. There are reasons for slowness besides malware - i.e. disk fragmentation, disk errors, corrupt system files, too many startup programs, unnecessary services running, not enough RAM, dirty hardware components, etc. As your system gets older it becomes filled with more files/programs and has a natural tendency to slow down so cleaning and regular maintenance is essential.