Here's just my guess.
The traditional singlecoils are both entirely through the pickguard (no metal over the tops), and have magnetic pole pieces, so the "important" part of the magnetic field mostly comes out of the top of the pole pieces, and the responding field from the strings goes straight through the coil without anything blocking it.
The P-90 is covered over the top except for the pole pieces, which in a P-90 are just steel slugs - they have a bar magnet under the pup like a humbucker. So you're blocking some of the magnetic field from the magnet by having the metal over some of the magnet (even though the pole pieces aren't covered), and you're blocking some of the magnetic field from the strings, which can't reach the interior of the coil because a good portion of the coil is covered by the metal pickguard.
I'd bet if you actually uncovered the P-90 (so that it's installed like the single coils) it'd work fine, or that if you just drilled pole piece holes for the single coils instead of through-mounting them as you did with the P-90 you'd have pretty much the same problem.