I can speak of a similar issue I've had. '12 Squier Telecaster. passive di into presonus 16.4.2. 4th string G, G#, A. 3rd string C, C#, D. But to a lesser extent. Only does it with chrome XL's. Both light and med nickel wound xl's don't. No noticeable boost anywhere on them.
When I use the notch filter set to 155hz with gain at -15db it all but eliminates it. I then lowered the E side of the pickup half a turn and got the same results. The level input before eq/pickup adjust would avg 2 db higher when playing those notes, but now avg +/- 2db over all the strings in the first 12 frets.
Hope this may help, Dave
Interesting, I tried a similar thing with my pickups last night, maybe I'll adjust them a little more and see if it helps.
I'm still really hoping it's not the Pyramid Gold's because I love the tone and feel of them. I would hate to see them go.