The MM lift helps take a bit of the angle out of the CV. With the belly up, you actually have the rear t-case output on a more upward direction. Increasing the angle on the CV, thus more chance of faster wear on components and resulting vibration.
You did put in a small body lift? 1.25"
The MM lift, small body lift and belly up all sort of work well together. Done this to several Jeeps. The MM lift has reduced and in some cases eliminated drive shaft vibes. Amazing what a few degrees can do