I had that problem after installing a Race VB and was told it was due to older electronics. I was told to call DTT and buy a voltage regulator for the 47re it cost me 75 bucks shipped and took about 20 minutes to install and fixed the problem. I still get a second gear start after a long highway drive but its because I dont have the voltage dialed in all the way.
1998 12v Regular Cab 3500 2wd 5spd, Boost, EGT, and FP Gauge, 4K GSK, Tork Tec Adj. OFV, BHAF, Straight Pipe Exhaust, KDP Did
2003 VW Jetta TDI, 5spd, SBC stage 2, TDtuning stage 3, T4 .205 injectors, PD lift pump