python 991 mts mode problem

My alarm is a Python 991 with a DEI 530T installed. So I finally figured out that my parking brake was not hooked up to the neutral safety wire in my 2008 Honda Civic Si which is why MTS mode would never work. . So I got it hooked up and everything is now working. Except for 1 problem. When I initialize the MTS mode, get out of the car and arm the alarm, the car shuts down like it's supposed and the remote indicates that MTS mode is enabled, but I notice that the lights on my door and window switches on both door panels stay lit up.  If I don't initialize MTS mode and just get out of the car and arm the alarm, the switches do not stay lit up, so apparently it has something to do with enabling MTS mode. Has anyone else encountered this problem? Does anyone have any suggestions as to why this would happen and how I can fix it?