I think I may have found a pretty major bug. I think that if you warp time in the tracking station or at the space center the plugin seems to lose track of time. When I warp in the tracking station the plugin doesn't seem to know how much time has really passed, so when I go back to fly the UT displayed by the new stock UT clock is ahead of the UT you can get MJ to display. The UT in MJ advances maybe a fourth of what it should have.

This is not actually a problem. This was actually due to the in game UT clock using Kerbin days, while mechjeb was using earth time.

This remind me I ll have to take the new option to use kerbin days into account