Car running rough after radiator replacement?

A few weeks ago, my radiator started leaking badly while on a road trip. We took our 2000 Mazda MPV to the dealer, who replaced the radiator and thermostat (we felt pretty comfortable with that, as they confimed an earlier opinion from PepBoys). We picked up the car and drove it home on the highway with no problems. However, once I got home and started driving around town, I noticed that the car would occasionally "hiccup" while stopped at lights -- just a second of rough running and then back to normal. This would happen more frequently when the car was cold, and it would stop if I put the car into park or neutral. It has been getting progressively worse, and I noticed it for the first time while driving up a hill yesterday (chugged along roughly the entire time we climbed). As this wasn't doing this before the radiator replacement, I'm wondering if the dealer could have disconnected something by accident? Any ideas on what it could be?