IIR correctly...
The pulse generator triggers the batch fire sequence for the fuel injectors.
The Motronic 1.3 on the BMW is setup to fire the injectors in two timed batches of three each. This is to more closely align the injector pulses with the valve track. The pulse generator is the trigger for timing the sequence.
If the pulse generator is disconnected the injectors fire in a single batch.
By most reports the difference is pretty minor. I can't think how the problem you describe is related to connecting / disconnecting the pulse generator. If you've had your fuel injector wiring off lately, you may want to check and make sure that all the wiring clips are firmly connected to the top of the injectors. I've seen problems (MARTIN!!) with loosely connected injector wiring causing intermittent firing.
Jeff
Bellevue WA
90 535iM - not much stock remains. 3.7 liters, ported head, cammed, 3.73 diffy, M5 brakes, MAFed, yadda yadda yadda
86 Porsche 951 - Track Toy