I tried to replicate here on my Windows machine here with the latest version of MiniMeters and the window remains where I leave it after quitting and reopening.
The "Reposition Offscreen Windows" setting moves a window back on screen in the case of a display configuration change. Such as removing a monitor. It may be worth turning it off and seeing if that fixes the issue for you. If changing that setting doesn't help, please try the steps listed here. If you're still having issues let me know and I can offer more assistance.