I have left them in manual mode for about a year before getting around to fixing them. I may just leave my '97 that way - it has a hard top anyway.
Here are some causes and solutions. I'm not sure that the alarm module will cause it to malfunction. Much more likely a faulty hand brake light switch, top relay module, latch microswitch, or mechanical problem.
https://www.renntech.org/topic/8961-boxster-top-wont-operate/