When you hover over the mechjeb gui list or any other mechjeb window the camera will follow the rotation of the current vessel if it is rotating. Moving the mouse out of the gui resets the camera to its initial position.

This only happens in the map view when flying a vessel. Tested with both x32 x64, normal and latest dev build, ksp 1.1

Just wanted to confirm that I get the same issue. Also happens if I tab away from the game regardless of where the cursor in game is.

This issue was fixed in the dev builds here d785d6b.
I can't release a new official yet since the bug with the orbit calls are still there. So switch to the dev build for now