CAMARO6 - Procharger Tuning HELP!!

I am posting this in 2 sections, Forced Induction and Tuning because it relates to both and I could use an answer quickly, thanks!!

Installed ProCharger and Kooks LT today and install went incredibly smooth. I'll be doing a write on soon. Question, though, the Procharger locates the MAF sensor in the pipe coming back from the intercooler into the throttle body which means a lot of forced air is coming over the MAF. I would thought it would have been in the filter pipe like is normal. We are getting an MAF code
and the tuner is having a hard time tuning. It looks like the MAF is in correct as it will only line up one way and fits the bolt holes properly.

Has anyone run into this issue? Is the tuner missing something I can relay to him?

Thanks