I be faaaarrr from a expert, maybe a dodgy switch - I'd guess out of phase pups?
But I'd try this :
Pickups both work? A resistance test is good, wiring up each pup to the output jack and testing is better.
Switch works? Continuity test when trying pos 2 & 3.
Pickups in phase? Read this -
http://www.neighborhost.com/scrapbook/pickup-id.html - and have fun figuring out which wires go where, when matching up the pups. I always run through Artie's little process when I get a pup - much less hassle than re-soldering :?