jeep jk 2011 viper alarm woes

Hey guys, I installed a python 574 (viper 5901) on all manual jk recently. Everything was working as it should, but recently I started to get a message on the key fob every time I arm within 10 sec I receive the message 'door open'. I got aftermarket door lock actuators that I hooked up the door lock 3-pin connector and didn't have an issue before till recently. As a result, my remote start will not engage. Any ideas?
The module is the 5x04 Im using a CHALL with firmware 2.11 the only cables I connected were... On the main harness the H1/1 H1/2 n H1/3 brown for siren. On the 24 pin harness the H2/2 neutral safety. H2/16 + brown brake shutdown imput. H2/17 grey (-) hood pin input and the H2/23 violet/white tach input. On the remote start 10-pin is the H3/1 pink (+) ign 1 and H3/7 pink/white ign 2. One of these goes to the CHALL. sorry for the long post but I wanted to be as specific as possible. Since I didn't use a clutch bypass, for the remote starter to work I have to engage the 4lo before activating as it doesn't require the clutch when engaged. Oh n when I armed the system it flashes twice then twice again...I figure twice once should be it but since it didn't give any problems before i figured it was good?

I tried disconnecting the door lock pin on the module and connected again...nothing...I need help please?

Well for the few of you who may one day be in the same situation, I just re-programmed the CHALL unit and everything is back to normal...I tried turning off the alarm menu 2 opt 4 door trigger error chirp and while I wasn't getting the message; my sensors and remote start weren't working bc the alarm still detected an open door.

I would check all the door trigger inputs on the alarm and the CHALL to make sure they aren't touching ground/12v (depending on the trigger wire) or another wire somehow that it shouldn't.   

Even if the CHALL was connected D2D, it's possible the harness is still connected for other connections and those trigger wires (although cut) may be touching a ground source (or another wire) that tells the vehicle or the alarm system that a door is open.

Yeah when I re-programed the CHALL I also re arranged my cables, all the cables that needed to be connected are either t-taps or solder together except for the hood pin cable that I soldered after reprogramming.