I ran into some problems when I tried to use mechjeb to make small adjustments to a satellite's orbit. The satellite had RCS enabled and several propellant tanks however when the maneuver note was reached mechJeb would not throttle up and keep skipping the node.

Had the same problem updated to the Feb 15th patch and it kind of fixed it

I just had this happen again with two engines one was a modified LF engine and the other was the ANT which is a stock engine. So it seems that there are some engines that simply will not fire which is odd cause if it responds to throttle controls it shouldn't matter what type of engine it is or which mod it comes from