The position you have the System Prefs on your screen when you close it should be stored in the plist file.
/Users/yourname/Library/Preferences/com.apple.systempreferences.plist
Thus, if you trash the plist it really ought to be created with the default position, but even that shouldn't actually be necessary: when you move System Prefs window to where you want and close it the new position should be recorded in the plist and used next time you open it.
The only thing I can think of is perhaps something is funky in the way your account is considering the dispaly. Launch the Displays preferences and try clicking the "Gather Windows" button and the "Detect Displays" button, check that Rotate is Standard, and also check the Arrangement tab to make sure it shows one display with the menu bar.
Francine
Francine
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