Is it a phase/polarity thing? Have you got a north magnet wound neck pickup and a south magnet wound middle pup?
I'll admit I don't really know what I'm talking about, but I seem to recall mixing the wrong polarity of single coils is bad. Reverse wound and reverse polarity is good as it's hum cancelling (like a humbucker), but I think reverse polarity and same winding would cause the problems you're having?