Any accessory that communicates with the class 2 databus can interfere with programming. If you have an aftermarket audio adapter that is tied into the class 2 databus, disconnect it or pull the fuse on it before using a programmer.
Even OnStar can interfere with programming. That's why most programmers instruct you to pull the OnStar fuse.
As Dragon mentioned, a weak battery will give you problems as well. As a matter of fact, GM just certified a battery charger to use while programming:
http://www.gmtechlink.com/images/iss.../TLjul05e.html
Do NOT use a regular battery charger during programming!