2001 Chevy Blazer chugging/surging

I have a 2001 Chevy Blazer w/ 114,000 miles on it. This past fall I noticed that it started to do this "chugging" at certain occassionally. I didn't think too much of it til it kept on doing it constantly between 50-60 mph. It feels to me like its "chugging" like there's a blockage or something. It only does it between these mphs & I noticed that when it does this, the rpm's seem to jump some to a (only a very small amount) as it is "chugging". We replaced the fule filter which didnt help so I took it to the shop today & they said that my transmission is slipping and to take it to a transmission shop. They also hooked it up to their computer, because the check engine lite is on & has been on for years, and the codes that came back had to deal with emission's and that wouldn't cause this "chugging" problem. The chugging isn't too hard but it is noticable, but it can be more noticable when it is colder outside. Is it really my transmission slipping or could it be something else?