Have you tried resetting both windows?
When you enter the car, lower the window slightly, raise the window to its closed position, let go the raise / lower button and then press the raise button again for about 5 seconds.
Also make sure your soft top is fully closed - the top microswitch may not be functioning corectly and confusing the system.
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2001 Boxster S (triple black). Sleeping easier with LN Engineering/Flat 6 IMS upgrade, low temp thermostat & underspeed pulley.
2001 MV Agusta F4.
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