Viper 5701 has me scratching my head

Battery in the truck (trailblazer) died yesterday. So, I charged it and it was fine (the truck has left me with a dead batt a few times over the last few years.....randomly but that is not what this is about). So I charged it and then took it for a drive all was well, now this morning the doors don't lock or unlock even though it chirps. It's not in valet mode and I can hear the relays clicking in the brain under the dash but something isn't right. I have put it in valet mode and taking it out, I have disconnected the control center and reconnected (I know it is sensing the remote but I had read diff things online and figured it was worth trying and couldn't hurt). Basically, I think maybe the XK01 module might have died because it won't start with the remote start and the alarm won't get set off by opening the door but the shock sensor will set it off. Also I tried the remote start one time and even though it didn't work, I started the truck and when I shut the key off and took it out the truck stayed running and then I hit the remote start for shutdown and it shut off the truck. Anyone ever seen an XK01 go bad and second, you guys think that is the issue? Thanks

Just a small update. I unplugged the XK01 10 pin and 4 pin connectors and then tried to reprogram the unit...........it now does everything it did before (never could get it to put the windows up), but now the remote is no longer a two way and I don't get the sounds from the remote. I don't know why reprogramming the XK01 would effect the remote but I will trouble shoot that next. I am just glad the functions work.