Problem statement.  My windows don't dip when I unlock the convertable roof.  I've already replaced the micro-switch, and the roof control unit in the footwell after this unit burnt out.
The windows also don't dip when the roof is down and I raise the roof.  Finally, the alarm acts erratically -- it chirps twice when I lock (it locks), but then if often starts to alarm for no reason.  The windows do go up though when I latch the roof after raising it.
Background:
I had the alarm, keys and ECU reprogrammed a couple of years ago, and had no issues.
The 
roof stopped working last year, which I fixed, ultimately replacing the microswitch in addition to the other parts shown in the thread -- although this issue described above has lingered.
Current fault codes:  Alarm I48
- 34: Status: Not present.  Passenger compartment monitoring sensor, short to ground.  Occurrence counter 1
- 33: Status: Not present.  W line (DME - immobilizer), open circuit.  Occurrence counter 74  
- 25: Status lead, signal converter, short circuit to B+.  Occurrence counter 127
Alarm I32
- 34: Status: Not present.  Interior sensor faulty, Not present. Occurrence counter 1
- 33: Status: Not present.  Interior sensor faulty, Not present. Occurrence counter 74  
- 25:  W lead, status - present.  Occurrence counter 127
I just pulled out the panel where the roof latches, and confirmed that all 3 connectors were firmly seated.
Any thoughts or suggestions?
-John