So which upgrade caused my tuning problem?

[Rockula]

It has been intonated with the new bridge - I gave it to a luthier to do a pickup swap (Fishman Fluence Classics sound outstanding in that guitar) and to intonate it with the new bridge (because I hate intonating guitars). Seems like he just didn't screw down the g string screw all the way.

Good choice. I have a very early production set of those in my best PRS. Really great tones available. There are also useful coil split and high frequency tilt switching options available by messing around with unused solder terminals on those pickups.