When running the options to limit acceleration and/or max throttle, mechjeb does not compensate for this when performing maneuver node burns leaving your adjustments significantly far from their intended parameters.

ie; if you limit acceleration to a value or cap the throttle at less than 100%, mechjeb starts the burn assuming you are letting it go full throttle which ends up meaning it starts the burn too late and finishes the burn much later than intended.

Similarly if a stage/engine runs out of fuel during a node, the TWR change isn't taken into account and the burn time prediction can be way off. Maybe semi-predictable by checking if remaining delta-V in current stage is less than delta-V of node (use starting TWR of next stage as rough guide for burn time after staging), though that won't help for non-staged engines running out of fuel.

I'll try to make the node execution know about throttle limitations soon. Making it know about staging is rather more involved. While doable, I think it would complicate the code too much.

Added burn time compensation for throttle limits. Closing.