I believe I am having this issue as well. It happens intermittently when editing a filename. After editing ends, none of the arrow keys or Finder keyboard shortcuts work. Interestingly enough, TotalFinder specific keyboard shortcuts, such as command-shift-right to switch tabs, still work just fine, but command-O or Enter do not. Clicking on another tab and then back fixes it most of the time, but not always.
This started a month or so ago and happened every so often, but recently it seems to happen every time I edit a filename. Let me know if I can do anything to help diagnose the source, such as sending Console logs or running special debug builds.