Pickups out of phase?

I played a gig last night with a fairly new bass that has a few issues.
The most glaring issue is uneven frets- and i already have an appointment with the Mouradians for fret leveling polishing dressing etc in three weeks.

The other issue is the pickups. It has an MM at the neck and a Jazz at the bridge.
I noticed a HUGE drop in treble output for the first two sets. Blamed the amp, kept tweaking my mids and highs on the 400+ which only helped a little.
By the third set i tweaked the bass. I know the fret level is part of the problem- but something weird happens with the J pickup.
Right before the J pickup is cranked, it gets this "out of phase" sound where the bass sounds underwater. In home practice this is simple, when i find that spot on the pot i dial away from it!

The temp solution last night right before third set was dialing the J pickup WAY back, almost shutting it off.
After this the MM pickup sounded full range!!! I got back all my highs and mids and could hear myself through the mix. Third set had lots of funk so this was important. Tower of power james brown etc...
Im gonna have the Mouradians check the wiring and pickup height , etc

Anyone else ever have a bass act like this? This is my first MM/J config. Passive no preamp.
Nukes

 

Cool thanks for the reply!
What about Laklands that have the opposite setup with J in the neck and MM in the bridge? Does that setup change things?
I can get the Mouradians to install a coil splitter thats a pretty easy fix.

 

J soloed sounds anemic to me, but to be honest thats how all bridge J pickups sound to me when soloed.
When Mouradian did the intake he said the pickups were installed at uneven height and i THINK he said to even output that the jazz pick up needed to be raised, in the MM pick up needed to be lowered.
The good news about the bass neck is that it straight as an arrow with a fully functional truss rod. if you knew the builder in question, Tom Martinson, you would know that this is good news LOL!
Right now I'm into this bass for $300 and I'm okay with being into it for another $300...the woodworking is a piece of art and it's very ergonomic and it plays like butter!
You guys are very helpful about pickup configuration! although I've been playing for 30 years I'm still kind of slow on the uptake about a lot of the stuff and thanks for the help.

 

You guys all have me curious so later today when I get off work I'm going to take the back cover off look at the wiring and pots and I might even take the pickup covers off. Martinson puts beautiful wood pick up covers over his pick ups so you have no idea what's under the hood, but I might give it a shot!

 

Passive- but im going to doublecheck.

 

These are the guts. Looks like pots and wires and one resistor- all solder joints look unbroken.
The suggestion of a stacked jazz was a good one! Makes since to have two humbuckers working in conjunction.

Going to Cape Cod for three nights. No bass . Gonna defer to Mouradian my tech in three weeks for pickup options!

 

So that would make the pickup essentially a P in jazz housing? You are right i mis-read your post sorry!