Hi Joe,
So it's not the color of the lacquer then - phew!
Maybe you sanded some areas more than others after the sealer coat/s (or over-sanded them, like Kent suggested)? If that was the case, then those areas may have soaked up the finish and given you this not-so-glossy look? If so, then the solution is the same as I suggest below....
How many coats of lacquer did you put on top of the sealer? Were they thin coats? What kind of spray equipment did you use? It sounds like you used pre-pressurized cans = expensive

. I'm just trying to get an idea of how thick the finish is already. Can you measure the thickness (with a digital vernier at a finish edge, say at the bridge or neck)?
What was your leveling sanding procedure? It could be that you didn't flatten the finish over the entire area (you know, keep sanding until you can't see any more shiny spots before moving on to polishing). That would leave areas that were less glossy than others. If you look across the finish at an oblique angle with a light behind the instrument, can you see shiny spots/islands in the not-so-glossy area? If yes, then what I'd do is go back to 600 grit and wet-sand the whole instrument again.
That's what I'd do from here if I were you. Go back and re-sand it starting from 600 grit, making sure that it's absolutely flat with no shiny spots, then move on up through the grits to 2500, then polish it on a buffing wheel. Basically, re-flatten and re-polish it from scratch. If it still has the problem, then you'll have to sand right back to bare wood and start over or you might get away with adding a couple more coats and re-leveling/polishing again....
Cheers,
Dave F.