N.J.C I guess I can continue to be snotty because I just talked to Tom this afternoon. It took me a while because he actually doesn't work where you got your remote start installed but rather is subcontracted to do the work. They gave me his cell phone number. He's a great guy really. We talked for about 20 minutes. He told me that in your truck (which he did remember you because of your theft light issue) he used the GMBP bypass from Directed Electronics Inc. which is made by Trilogex. Here's a link to it
http://bypasskit.com/product.aspx?prodid=GMBP He stated that you must have misunderstood what he told you. Yes, it is hooked into the OBD2 connector but he didn't use a scanner or programmer to disable the passlock. This now makes since why it starts fine remotely but has the theft light on if you use a key. The GMBP does use computer logic to bypass the security system but it actually sends out the correct code via the data wire (pin #2 in the plug) to the BCM. If it were simply a programming thing why not correct it when starting with the key??? Why only would it be correct when starting with the remote starter???? This part is where I got lost in what you said before.
I then explained what I've been up to and what I've found out about these Passlock issues. He was actually excited to hear what I've done to bypass these faulty systems so much so he put my direct number in his contacts page. This way if he gets stumped or has an issue he has a better source of information instead of those from DEI (which is the brand or remote starters he uses).
So the end result to completely rid you of your problems with the theft light you should do the resistor trick that I've talked about. This way no matter how you start your truck (nice truck btw, I had one before and loved it) the light will not be on as you drive.