Stupid question, but you've dicked around a bunch with pickup adjustment, right? It usually takes me weeks of playing around with pickup position before I'm happy, backing it waaaay off, bringing it up too close, changing the angle of the pickup, etc. I think you can also mess with the pole pieces on the MFD as well, right? (Flat vs a vintage stagger is a difference that may or may not work better for your ears.) The changes can really alter how a pickup sounds and feels.
I do this all the time!
New pickups, especially ones that aren't the norm, mess with my ear's sonic expectations.
Case in point:
I like a5 pickups mostly, apparently. I picked up (no pun, lol) a set of dark matter 2s (ceramic mags) from dimarzio on black friday.
When fired up, I heard this weird attack thing that was like an upper mid spike, but only affecting the attack, and only on the top 3 strings.
So I adjusted everything. I lowered poles, radically tilted it, etc.
Better, but.......eh.
Put it down and walk away
Came back next day and tweaked some more. This time with my amp models.
Ill spare the whole rundown, but suffice to say, it took a few days for my ears to "accept" the DM2s, and also to figure them out.
You know how they were ultimately set? Even, but slightly elevated poles (just a hair above the bobbins) and level!
I wouldn't have believed that based on my initial reaction. Lol
Now, its down to overall height adjustment.
I have 3 weeks to figure out if they're staying or swapping.