Yes, cache folders contain lots of files that don't really need to be scanned. If you are dealing with a possible infection you should disable all caching until you have eliminated the treat (maybe take this opportunity to measure the page speed with caching enabled and then turn caching off and empty the cache to see if it is even helping your site's overall performance). Cached content can cause inconsistent results making it harder to determine the source of the infection and whether or not the infections have been removed.
Alternatively, you can add the cache folder to the list of folders to skip scanning and my plugin will finish the Complete Scan more quickly, but you would still need to empty the cache anyway because it could cause the infections to display on your site even after my plugin has removed the threat.
Please let me know if you need any more help.
Aloha, Eli
