No Problems
I have just changed the stereo head unit in our Boxster 2001 2.7 manual. I left the key in the ignition for at least 15 minutes and didn't experience any problems. I have had keys fail thought. The key is made up of three parts blade, remote control to operate doors/alarm and immobilizer tag. I would guess the electronics to communicate with the key fob when the key is in the ignition must be below the steering column. Maybe you have disturbed this wiring in fitting the stereo. have you tried the spare key?
I hope this helps.
Regards
Paul
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