Hey!
Sorry you're running into this. MM is supposed to return the windows to the position they were when waking from sleep / disconnecting and reconnecting monitors. Would you be able to reproduce the issue then send the "last_run_log.txt" file to support@minimeters.app? That would be super helpful.
You can find the log file by following the instructions here: https://minimeters.app/help/manually-send-crash-report/