Fault in security system

As a preliminary, You need to see what diagnostic trouble codes are stored in all the vehicle systems. This will require a specific tester, and not just a code reader, as those are responsible for obtaining only powertrain codes. The radio/air/and windows should have nothing to do with any security function, vehicle or content theft. It does suggest a possible class 2 communications fault, as a loss of communications will cause like symptoms, and may even cause the IPC to illuminate the sucurity light. I would suspect a code check would reveal U-codes in multiple modules, confirming a possible fault in the data link. It could fit into a category of a wiring problem, a power/ground fault to a module, or a corrupt module, and may only be inter-related to the security system.