There is actually an option to exclude folders from your scan and it is for this precise reason that I made that option available. Perhaps I should make it a default setting to exclude the cache folders but I fear that would lead to hackers putting all there malicious scripts in your cache folders.
A better work-around for you is to clear the cache and make sure those folders are empty before you start your scan (this method also ensures that any threats you remove also get purged from the cache).
Personally I recommend against using caching plugins at all. I might be opening a can of worms here but I wonder if you have ever actually measured the real-time page speed of your sites to compare the load times with and t=without caching enabled?