I'm wondering if someone could point me in the right direction to a problem i have!

I recently changed the engine in my series 2 for a rebuilt one.
Everythings running in fine, yet sometimes when i stop the car after a run it wont start!

It sounds like the starter motors not turning over as fast as it can go. But heres the strange bit!!
If i unplug the black fuel ECU and plug it back in it turns over normally and fires first time.

Can anyone shed some light on this as its very strange. Mabye a sensor somewhere that might cause this? im guess by unplugging that ecu it must reset everything?!

CheeRS

Matt