1997 Hyundai Tiburon 1997 Tiburon, Running Rough

Recently, my 1997 Hyundai Tiburon overheated and we found out it was a crack in the radiator. A friend and I replaced it and it ran perfectly fine for about a week. This morning, when I came out to my car to go to work, I started it up and it was running extremely rough. I ran it for about 30 seconds and as I was about to shut it off, the check engine light came on. I got out, checked hoses, cables, and fluid levels and everything looked fine. I got back in my car and started it up and it ran normal, but the check engine light was still on. Having no choice, I drove it to work and parked it. Aside from the light, it had no problems. I got off work and came out and started it up, Rough again. I shut it off, checked under the hood and again found nothing. I started it back up and this time it ran rough for about 5 seconds and then started running normal. I drove it home and parked it and checked everything. Except for the check engine light still being on, it seems to run fine on the 2nd startup each time. Is there any way that this problem could be linked to my new radiator, or am I looking at something much worse?