I was going to suggest that maybe it was the scale length 25.5 vs. 24.75 but the Jackson (25.5) and Explorer (24.75) are both of these respectively. So that theory may be out. I know I have a lot of guitars and when I switch back and forth a lot it makes it hard to forge that "relationship" with just one. I find myself confused as to which one I like best. In fact, Im in the process of preparing to thin the heard by selling about 4 of them to have one custom shop made that encompasses most of my favorite specs all into one guitar. That is why I am here. I know it wont be the same as each has it's own unique quality but, I'm gonna try to have it all on one strap.
Then.. adapt and accept it for what it is. CUSTOM SHOP BABY!!!