I'm not sure if this is the reason, but I remember reading either on this site or at http://www.guitarnuts.com (great site) that your pickups need to have the correct magnetic polarization in relation to each other. That is, it must be a North or South, depending on what the rest of your pickups are.

From what I remember, the pickup polarizations need to alternate, e.g. Neck = North, Middle = South, Bridge = North (or vice versa).

If you do a search on this site (maybe try "north") or lookup the guitarnuts site, you might find out some more info.

Again, I'm not sure if what I just said is the reason for your problems, but it doesn't hurt to do some research on it.