i don’t know when this started happening, but in the current version of TotalFinder when in dual-pane mode, all the go-to-folder commands in the ‘Go’ menu of the Finder are directed at the right-hand pane, even if the left-hand pane has focus. this happens if you use the mouse or the keyboard shortcuts.
oh, and the longstanding issue where the Finder window with focus is sometimes hidden when switching apps is still present as well. when switching to another app and then back again, the Finder window which was previously on top and with focus sometimes ends up behind other Finder windows.
i’m on OS X 10.10.5.