02 civic ex obd2 scanner tool question?

I just finished swaping in a new engine (I swaped in a hx instead of a ex) in my 02 civic ex and for some reason it wont start unless the obd2 scanner tool is hooked up. If i take off the obd2 reader while the car is running the car dies after a minute and i wont be able to start it up anymore. Once i hook up the obd2 scanner tool, the car starts right up. I work on cars and this is a 1st for me. It sounds weird and i have taken it to the shop and they still cant tell me why it does it. I just assume its something electrical. I dont know if anyone else out there may experiencing the same problem.Let me know thanks