Hi,
I'm having a very interesting issue with MechJeb. Currently, MechJeb will not control my craft unless my mouse is hovering over a MechJeb window which activates the InputLock. My normal in-game SAS also will not work unless my mouse is hovering over one of these windows. Occasionally it'll randomly work, especially if I toggle the manual input lock, but it is unreliable and will randomly stop working at the most annoying times. I've tried reinstalling the game, and I've tried running with no other addons, but I haven't had any luck in fixing this issue. My only other addons I'm running currently are Connected Living Space, Ship Manifest, and Module Manager. When I reinstalled the game I installed MechJeb first and made a new savegame, and still had the same issue.
Here's a link to my log file https://drive.google.com/open?id=0BzuxLXaOCmQgclhoZTFOdV9qa00
Let me know if I can provide any more information to help with this issue.