Compatibility Issues with WordFence

Hi, we use WordFence as our security and scanner. Last week we started having an issue that the scan would take over 3 hours to run instead of 10 min. I contacted WordFence support (we use the paid version) and they determined that the problem was a gigantic number of files being stored from W3 Total Cache here- */cache/page_enhanced/* which would take the scanner so long to get through that the scan would terminate automatically. When the support person had the scan skip */cache/page_enhanced/* the scan proceeded just fine. I don’t want to leave that cache folder unprotected though- anyone have a suggestion on how to manage this?
Thanks!
Abigail