It seems that using the new Sepatron boosters, placed on the same stage as the radial decouplers, is breaking the auto-stage function in the ascent autopilot. (unless I did something wrong, it was 3am after all ;)
Mechjeb doesn't seem to want to use the new higher wapr options introduced in .16. This makes using Orbital Operations to other planets pretty painful.
Whenever I have a mechjeb part on a ship, even the simplest ship possible (command pod with a mechjeb module on top), I get an incredible amount of messages in the debug console (they fill the window within about half a second or less)....
After the .17 update, and even with 1.9.2, Mechjeb thinks thinks north is west and visa versa. I havn't tried yet to see what it does to east and south. When I try to trans to any planet, even Kerbal, it just sits in solar orbit with no idea what...