OK, so. I had the same problem as a few people in this topic; the one where Mechjeb wouldn't show up at all except for the AR-202 unit. Now, I'm going to go ahead and assume all of us with this problem are on Windows 8. Microsoft pulled yet another dick move w/ W8, that being that all the files on your hard drive belong not to you, the user, but to the Trusted Installer user. And because Microsoft hates DLLs, this system is blocking KSP's access to the MechJeb2.dll file. I used the take ownership ability on the folder (link here: http://www.howtogeek.com/howto/windows-vista/add-take-ownership-to-explorer-right-click-menu-in-vista/ ) and then MechJeb (and a whole bunch of other mods) started working perfectly, regardless of install location. Hope I've helped someone!
