Okay. It's really only an issue with the boosters, B9s heavy lifter engines, and some of the more powerful engines. Mostly the boosters and those heavy lifter engines. Also, a possible issue I'm noticing, when I tried to use the landing guidance to land at either the VAB roof or the launchpad, each time (two or three times) it tried to do a landing, it was over 3km off target. I checked with a regular 'pick target on map' landing and it got it within a kilometer. It might be because my 'lander' looks like this: Which is just a pod with science stuff on it that I decided to slap an RCS tank and RCS nodes on so that I could get more precise biome landings. Not sure why MechJeb doesn't use RCS in atmosphere to fine tune the landing precision.