Well, I think we found the fix for my truck setting the P0622 code. During the install of the ATS Trans Commander the wire for the aux power for the transmission relay was hooked up. After a few calls to the trans installer and ATS it was decided that this wire does not need to be connected for the 47re but does for the 48re. This morning we disconnected the aux power, disconnected the batteries to clear the codes in the pcu, reconnected the batteries after about 20 min with the key in the 'on' position. Turned the key off, reconnected the batteries, checked for codes, P0622 gone, started the truck, turned the truck off, checked for codes, P0622 still gone. CEL light now goes out after starting the truck. Code is still gone. Have started the truck over ten times with out the CEL staying on.
So, it appears that if you have an aftermarket way of locking up your tc, check to see if you have aux power going to the trans relay, its under the hood in the fuse box. I could hear mine switching with the key 'on' but not started. By removing this from my truck, I eleminated the P0622 problem.
Time will tell if it is a permenant fix.
Casey