Mouse doesn't work in TotalFinder

I apologize if this is a duplicate but I have looked before and found nothing similar. I was OK with the problem persisting until now and I’ve had enough.

My issue is that intermittently I cannot select a file by using the mouse in TotalFinder. I can navigate with the keyboard, but this is inefficient a lot of the time. Occasionally it will come back after I open a file using the keyboard, but that is a pain. At this point, I’ve put up with the problem long enough to report it and see if there is anything I can do about it.

I am on OS X 10.9.5 Mavericks with a MPB 2.7 GHz i7 with 16 GB RAM. I have lots of things running all the time on my computer including Dropbox, Memory Cleaner, TotalSpaces, and BetterTouch Tool (which is no deprecated but still fantastic). If you need any more information, just let me know. I hope there is something I can do to fix this.