Here's a couple of things to try.
First, the easiest way to identify which pickup is active and what the pickup selector switch is doing it to gently tap the top of pickup with a metal screwdriver while amplified. When you tap on an active pickup, you'll hear the tapping sound through the amp; if the pickup is not active, it won't be amplified.
You were already in the ballpark when you took a look at the gain trimpots on the EQ board. I'd try setting them both at midpoint. If you situation is as you describe, one of the pickups will be much louder than the other (you can determine this in the both pickups on position or individually by flipping between the bridge and neck). Pan to both extremes and remember which end of the rotation was the louder pickup.
OK, now unplug and swap the pickup connectors on the EQ board. When you do this, the bridge pickup will be running through the neck pickup's electronics path and the neck pickup will be running through the bridge's path. Pan to the extremes and note which end of the rotation has the louder sound.
If the louder sound switched to the other end of the panpot rotation, then one of the pickups has lower output - if it's not a faulty connection on the pickup lead, then the pickup may need to be replaced. There's no condition where a defective pickup will get louder, so the quieter pickup is the one with the problem.
If the louder sound stays in the same end of the panpot rotation after you swapped pickups, then the problem is in the electronics. This could be a broken panpot, broken trimpot, or a problem in the EQ board.
It's not covered directly in the Spoiler FAQ, but it sounds like the Spoiler only has a single preamp (e.g, it's amplified after the panpot blends the pickups together), but I could be wrong on that. If there's only a single preamp, then that won't be at fault, but if there are individual preamps for the two pickups, then one of the preamps may be bad.
Good luck in your hunt,
David Fung