Brian.. it's not supposed to work. I didn't do a swap ever with an 03 using anything but an 03 for that very reason. Never really dug into it though. Dave and others said 03 was the unicorn year and that's in all cars. First heard about this on Bonnevilles, and it applied to all platforms with the 4T65. Might be worth a call to TEP to triple check though.
Here's what I do:
If you have a 97-02 use a 97-02
If you have an 03, life sucks use 03
If you have an 04-08 use 04-08