The little lights on the inside of the door that should warn a thief that the alarm is active...they don't blink now, but rather are full red and on.

Any ideas?

 

Gremlins occur when electrical changes are made - frequently. Sometimes it's because there are impedance changes in the system - and everything is inter-connected. The system recognizes the current changes. This May, or may not, be the issue. Does the alarm work?

 

The alarm system is connected to the factory head unit. When an aftermarket unit is installed, the alarm connection needs to be grounded, or the alarm system thinks that the head unit is missing. Do you know if your installer properly addressed this issue?

 

Not that this helps, but did the same upgrade to a Pioneer unit and did not have this issue. The speaker wires were all that i changed, the exact same power connector was used to the stereo....have you searched the model number to see if the issue comes up?