I am using TotalFinder 1.4.18 on OS X 10.8.4 (Mountain Lion).
Anything that causes Finder to crash, and thus requires a Force Quit of TotalFinder, results in Finder reopening without TotalFinder relaunching. After manually restarting TotalFinder, Finder selection doesn’t work, alt-tab doesn’t work, selecting application windows doesn’t work. When I say “doesn’t work”, I mean that generally it briefly highlights the “selected” item but the focus doesn’t actually stick to the selected item. The only fix I’ve found so far is to restart the machine.
Finder.app crash brings down also TotalFinder, because TotalFinder code is injected in Finder’s process. Yes, in this case system launches Finder.app again, but TotalFinder is not injected again by design (I don’t want to cause continuous crashing in some pathological cases).
Some people are reporting that sometimes first time after opening TotalFinder, windows are not clickable. Usually CMD+T, CMD+W fixes the issue as a workaround. You may also force quit Finder.app via CMD+OPT+ESC, wait for Finder.app relaunch and open /Applications/TotalFinder.app to re-inject TotalFinder into clean Finder.app. This time it should work without a need to restart machine.
I’m sorry for the issues. This is a timing bug and it is very hard to catch. It has happened only few times on my machine and never I was able to really track it down