Please install the new beta and you should be no longer experiencing that problem:
http://totalfinder.binaryage.com/beta-changes#1.6.27
I have implemented a different mechanism under Yosemite. It was needed to fix this issue:
The new solution:
Instead of defining tracking areas and keeping them updated, I observe all events coming to Finder windows. And depending on mouse position, I enable or disable Finder’s “mouse transparency”. This approach is more robust, because I don’t keep any state. I always act depending on actual situation and Finder cannot stay stuck in transparent state, because mouse activity will trigger re-evaluation.