My buddy has an '06 LLY with AFE intake, magnaflow exhaust, and Triple Dog. The truck runs great and he says it shifts great except for, iirc, the 3rd gear shift. He said he had heard (but can't remember what or where:p: ) this was due to some sort of safety feature from the factory for the trans and there is an electrical compnent to over-ride it.

Anybody know what this may be? If not, is there a way to "fix" this shift?

I think a Transgo Jr. would help. Another option could be the ATS co-pilot.
You can change some parameters with EFI live, but I'm not sure that would give the results you are looking for.