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).
http://mumechksp.userecho.com/s/attachments/201209/i_140.png
Here's the ship I was using:
http://mumechksp.userecho.com/s/attachments/201209/i_141.png
I tried to track down that error, and Google pointed me toward MechJebModuleILS.cs and MechJebModuleRendevous.cs which both contain the string "navball.waypointtarget".