My CTIS issue was this:
5 flashing lights and wouldnt inflate front rear tire on passenger side at DRMO. Manually filled to 60psi at the base fuel station, took three complete cycles. Drove 230 miles home to Wyoming and everything held air but no working CTIS. While troubleshooting the system and rebooting (disconnecting barrel connector at ECU), reconnecting then starting I changed to 4 lights. Leak checks all over the place, and I found nothing. My air dryer's bottom wasnt getting hot and outside temps were between -5 to 35F depending. 4 lights should be a leak but I believe it is any pressure error that makes a full loop check. This system is trying to equalize at a certain PSI.
I could get the system to try and work but never deflate, just went to 4 light after a while. I found the small filter/separator that is inline right before the in cab control box to have been Gerry Rigged. The bottom petcock was broken off so a screw + RTV was sealing the petcock hole. $15 later and a C&H unit from Tractor Supply had replaced it. These are generic 150 PSI rated units that mount on home air compressors. The stock one I took out was rated to 230 PIS but my system doesn't get over 130 PSI. Old one did have some dried debris in it so dont skip it!
I read 400+ pages in the TM to include the CTIS portion. While good it's theory of operation is wrong. Here is what I know now:
They system starts and gets to pressure. At that point it sends out a loop test, if that fails 5 lights error. If it passes the loop test but cannot equalize the system to the selected mode, 4 lights error. The TM states many times this is a leak condition, but thats only half of it. The HWY mode wants 55-60PSI my tires were set at 72PSI by DRMO giving noticeable height ( and road bounce!)over the one I filled to spec by hand. The 4 light condition shut the system off since it couldnt equalize to the 55-60PSI it was looking for. I'm sure this is a safety to not keep inflating a tire past safe levels. So in short 4 blinking lights is not always a leak.
What I found was the truck has the CTIS disabled by Maint at some point with valve stems in the T that goes to the tire from the hub mounted valve. I read in the TM that trucks used for heavy loads had to have their CTIS disabled by Maint, and I guess this is how they did it. These valve stems let the system fill but prevented them from deflating via the hub mounted valve.
Solution: Use a 9/16" open end and pull the input line from the T off and unscrew the valve core. Wait for lower PSI from tire and reinstall just past snug. You will need a 3/4 socket and 1 1/16 socket to get the covers off too.
I then had all six tires very low but not on the ground. Rebooted the CTIS and started the truck. The CTIS started and began to fill about 1/2 way and errored out 4 lights. Restarted the truck and hit HWY filled to HWY mode without a hitch. The system failure I believe was since the tires were all that low it got a leak signal and shut off CTIS.
I aired it down and back up 3 times and have let it sit overnight now with no problem. My CTIS is fixed!