When using landing guidance in atmo, MechJeb tends to overshoot target with heavier craft, SSTOs most of all. Think this may be due to miscalculation of drag effects, as fine tuning design to increase drag on larger craft greatly increases MechJeb's accuracy, but not the issue at hand here.

Issue:
When seeing that ship is overshooting, if abort the autoland and attempt to bring it down the rest of the way manually, throttle controls are locked out. Reactivating guidance using "Land anywhere" allows MechJeb to control throttle, but overshoot is unavoidable then. Manual throttle control remains locked out regardless.

Have tried aborting, then closing guidance panel. On some craft this may occasionally restore throttle control, but not reliably. No other mods installed. Clean install except for MechJeb and Module Manager.

All other landing guidance functions, e.g. deorbit burns, midcourse adjustments, chute deployment, etc. are working normally. Final descent rate adjustment is particularly spot on!

Edit 5/3: Further testing seems to show the issue is that the 'Limit Q' setting for Ascent Guidance is also being applied on landings in atmo, despite the direction of thrust being retrograde, i.e. preventing one from manually intervening in a landing sequence and using the engines to more rapidly bleed off energy and/or to shorten/steepen the landing trajectory. I don't know if this is intentional, but the simple workaround is to pull up Ascent Guidance and disable the 'Limit Q' setting before using Landing Guidance, since it does absolutely nothing for a standard aerobraking descent anyway. Also, if it is intentional, as a feature request it might be good to add a radio button to the Landing Guidance panel to toggle Limit Q, saving the minor tedium of having to access two panels prior to every landing in atmo. (I do this a LOT, because I am very fond of SSTOs.) If it is unintentional, then I suppose the Landing Guidance code should be tweaked to ignore the Limit Q setting. Obviously a very low priority either way, since it has such a simple workaround.