I am having this exact same issue with the current MJ version. I have noticed that it happens 95% of the time when I am using a probe-core for control, as opposed to a command pod (which then has a failure rate of about 50%). I have tested this on all the major planetary bodies, as well as Minmus and the Mun. If I select a specific landing location, or if I hit "land somewhere", MJ will correctly perform the burn to exit it's orbital path, and will then correctly angle towards retrograde (+/- some if corrections are needed). However, after this step (ship is currently on a sub-orbital course towards the surface) MJ will stop throttling the ship completely. The Landing Autopilot will read "final decent xxxxxkm". The Autopilot will then allow the ship to crash full-on into the surface and explode, without slowing down or correctly positioning for landing after the final decent stage. The Roll/Pitch/Yaw controls still show use as normal, however there is no thrust control again. If I cancel the auto-pilot, intentionally incorrectly orient the ship, then re-engage the autopilot -- it will correct orientation, but will still not thrust what-so-ever. Been at this for a long time, so yes, I have fuel, the required Delta-V, electrical power, etc etc. At first I assumed it was a conflicting mod, as MJ has almost always been very good to me; but then I removed all mods but MJ and started a new game to test it out, and got the same results. A couple times is seemed to get stuck on the initial be-orbit burn, and would just keep burning on forever past the initial Delta-V requirement until I took over with manual control. Perhaps it's getting stuck in a loop somewhere in the landing guidance code -- but Lord knows I don't know jack when it comes to this stuff.