2nd gear stuttering problem

My girlfriend just recenly bought a 2001 Jetta (http://www.volkswagenforum.com/m_2391/tm.htm#) VR6 with 80k miles on it. She had some work done at the dealership when she bought it (thats a whole other huge painful story)and while driving it home she noticed the Check Engine light was on. The next day I went out to drive the car and see if I could spot anything. I noticed the light was off when I started it up so I took it for a drive. As I was driving I noticed that when I accelerated in 2nd gear there was a stuttering/slipping problem and the check engine light would flash off and on occasionally and on then go out when I shifted into 3rd. Anybody have any idea whats wrong? Thanks in advance.