Well I've heard back from Superchips and it's no surprise that they are saying it must be the car at fault! They did however say that it was a very odd set of circumstances.
I really don't know, it's confused the hell out of me. I guess the only way I'm gonna get to the bottom of it is to let the professionals have a look, but as the car is performing perfectly I'm reluctant to do this as I don't trust any of them!
I wish I'd never bothered with this modifying malarkey as it's nothing but trouble. I guess it goes back to the old saying "if it ain't broke don't fix it".
If I do ever find out what's going on I'll post it on here.