it is a bug, and there is a way to fix it. i know the secret is buried in this forum somewhere, but i unfortunately can't remember the exact thing you have to do to fix it right now.
so rest assured, yer not crazy, yer mpc is not broke, its just a little bug.
the fix is something like, go to a different screen and then back, and it works after that...hopefully you'll find it or someone else will chime in.
edit:
i'm not sure if this is the same bug, but this is what i was aware of:
viewtopic.php?f=1&t=1854&hilit=note+variation+tuningLastWord wrote:I haven´t been so involved with this site so I don´t know if this issue has been dealt with before. It´s a pretty silly bug but it was a big problem for me before I found the answer:
PROBLEM: Sometimes when I use the 16 levels button to have one sound pitched over the pads my 2000XL won´t let me change the "original key pad" (default is 4).
THE SOLUTION: Press shift and the "Note variation button, AFTER". Assign the same sound to the "note variation" slider and then deactivate AFTER. Now 16 levels tuning work and the "original key pad" can be changed!