Yup, just a case of some 1's and 0's not matching up. No big deal. If you have a Competent auto locksmith around, they can do it for you (for $350~500). Heck, if you have a local electronics repair place, you could simply swap the immobilizer chip from the original A/T to the M/T ecu (simple chip desolder and resolder, they need to be able to deal with surface mount chips but that's common stuff these days). For under $100 you can buy a cheap hot air and soldering station that will do the job (600f temp for the flux used) and DIY. No need to even deal with programming, which was the bigger headache IMHO.

This is a tiny little speedbump with the right knowledge, you could have it sorted in under a day if you have the right local resources.

Worst case, I can help out (just south of Atlanta, so would take shipping).