What you are seeing usually occurs after using the software with a secondary display connected to your PC, and then later using the software again after you disconnect the secondary display. The TD doesn't know the secondary display is no longer connected, and because it can be configured to remember where dialogs open and always reopen the same dialogs in the same location (or always open dialogs in a specific place, like on a secondary display), the TD is still opening those dialogs where the secondary display used to be.
To correct this, after the TD starts up press Ctrl+Alt+Shift+R (that means press the R key while holding down the Ctrl, Alt, and Shift keys). This should cause the currently open dialog to recenter itself onto your main display. Hopefully the currently open dialog is the Settings window. If not, close whatever dialog you see and repeat. Once you've got the Settings window visible again, go to the Preferences tab, select the Display Management category, and change the preference that controls where dialogs open (top right of this page).
If you are using version 3.3, you can press Ctrl+Alt+Shift+F12 instead. This will automatically recenter all open dialogs onto your main display, and change that display preference for you.
I've got an idea in the works for addressing this in the next version.