Weird no start issue

Hello all. I have a 95 Mustang Cobra and below explains my problem. I'm hoping someone can help me diagnose the problem.

With the stock ignition system, the car won't start with the spout connector connected (i.e. computer controlingtiming events) but the car will start and run with the spout connector disconnected (i.e. computer out of the loop). :screwy::banghead:

Now the weird thing is with the MSD 6AL ignition system connected, the car will start and run with the spout connector connected or disconnected. :screwy::banghead:

I'm leaning towards a bad computer but just wanted to see if anyone has ever experience a similar problem and got a fix for it.

Thanks for any help.