I think it's a combination of things. I think the JB can't handle downtuning very well and since it's a hot PAF with an Alnico pickup it really struggles with tones that require a tight low-end. I think the theory that the pickup is too close to the strings is a good one as well, but like it was stated earlier in the thread, it's really hard to actually adjust that. Finally, I put 12-60 on it for C Standard and I'm realizing that was a serious mistake as it makes the bottom two strings unbelievably muddy. Devin Townsend has always talked about using the lightest strings you can get away with solely for tone and I think he's on to something.