On about a daily basis, I get into a state where the UI is completely unresponsive to input (though Tixati seems to still be functioning). When I try to click on Tixati I get the Windows bell as if there was a foreground window or alert box preventing control from switching back to Tixati. Any ideas?

Are you using 2.28?  They fixed something about this recently I thought...

If you try to resize the window, does that get it back?

How about if you go to the tray icon, right click, and go to Layout > Reset Windows?

I just upgraded to 2.28 about a day ago and haven't noticed the bug yet. I am not sure but I don't think I could resize the window. Resetting the windows would fix it temporarily before. I'll report back on whether I am still seeing it with 2.28. Hopefully it is fixed!