Did you try exporting that registry key after exiting UR (when it does save the position properly) and creating a batch file (i.e. UR.bat) with commands like:
regedit /s c:\path\to\exported.reg
start ultrarecall
to start UR (disable the auto-start option in UR [also make sure minimize at startup is unchecked] and place a shortcut to the batch file in the Windows Start Menu Startup folder)?
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