This has happened before, but I finally got "bug"ged by it enough to report it.
I’m running the latest build, 1.6.27, and this is a repeatable event.
After TotalFinder launches, the first time I select a “reveal in Finder” type command from another app* I get an unselectable window with no chrome in the default centre-of-screen location. It will not accept a click, and there are no window widgets visible, but if I Cmd-~ switch window focus, I can get to it and navigate by arrow, or close by Cmd-w.
The window goes into the background, and it comes to the front when keyboard switching to the Finder or Bring All To Front, but it is aberrant behaviour and I consider it a bug.
I am running Yosemite 10.10.4, fwiw.
*e.g. after completing a download in a browser, selecting the download and doing a Show in Finder, or Ctrl-click -> Options -> Show in Finder on an app in the dock.
Cmd-Tilde works to switch window focus in every app - it’s system wide.
Additionally, one of the reasons to use TF is the tabs - I create a keyboard shortcut (System Preferences - Keyboard -> Shortcuts) (Lo siento, no se en español) for “All Applications” then “Select Next Tab” and “Select Previous Tab”. I use Cmd-[ and Cmd-] but on a Spanish keyboard something else would probably be more convenient. That works in nearly everything, TF, Safari, Chrome, etc., most apps that uses tabs. Very handy.
And for selecting previous/next tab, be it in TF, Firefox, etc., I use JiTouch, a little app that allows to define more gestures in my trackpad, so I can use, for example: touching with one finger and tapping with the one at the right brings me to the next tab; touching with one finger and tapping with the one at the left brings me to previous tab, so I don’t even have to raise my hand from the trackpad.