Synchronizing subfolders - Slow

I’ve used eM Client for a while and love it. One thing that is frustrating is that after a period of time the “synchronizing subfolders” starts going through every folder in detail every time the program is opened (re-indexing everything like a first-run). Normally it goes through this process super-quick but when this issue starts it takes a lot longer than normal. A re-install (not “repair”) cures it but it does return after a period of time.

Is there something inside or outside of the program that causes this change?