Currently I assume it's a bug, if you're over the 10/10/10/10 cap and you play and complete a RJ mission you actually lose Instrinsics!!!! I played 1 Gian point mission to try out the new weapon balancing and I went from 588 ->583 once the mission was complete after checking in my profile.

TL;DR; If you're over the 10/10/10/10 cap do NOT play RJ.