Using lt1 edit I shut off all of the egr functions and the ses light still goes on and off with the cooling fan.. any ideas?

 

What is the DTC #?

 

Well, the fans will come on whenever there's an SES light setting code, so maybe you're looking at it the other way around. I bet you have another code/problem you need to disable/solve.
Take it to a place like AutoZone and get it scanned so you know for sure.

 

Doesn't pcmcomm come bundled with LT1_Edit? Can't you pull up the DTC codes with that?