Neck pup twice as hot...
I have an Alleva Coppolo LG (jazz style) which has an active preamp.
This problem happens both in passive and active.
When both pups are on, it sounds fine. When you roll back to bridge, it sounds fine. When you have neck up and roll the bridge off, suddenly the neck pup output is about twice as hot.
The pup placement certainly isn't the issue, it sits pretty low.