Jazzy, I am dealing with a similar problem right now with a Mesa Walkabout/Scout 12 (x2) combo. A little while ago, I started getting a midrange-y distortion, particularly around pitch of the open G down to the C# below it. Initially I thought maybe it was just weird cab harmonics or even a bad case of rabbit ears, but it's definitely there, and especially noticeable using my Persuader at lower volumes. After a lot of A/B'ing, I determined that switching to a different head eliminated the distortion. Most of the logic pointed toward a preamp tube flaking out, but after switching out both the Walkabout's preamp tubes with Mesa 12AX7's didn't help, I sent it back to Petaluma to be checked out.
Will post here how it turns out. Good Luck meantime... I know what you mean though. Fuzz is okay if you're into it, cool if you need it, but it is a major nuisance when you want clean.