Game bugged out on me as well; resetting helped until I hit the first kongpanion selection on the upgrade map, which caused the bug to start up again. In case others have not summed the bug up, here is all I experience:
*No longer able to use the keyboard to enter commands
*No longer able to use power generators
*Cannon locks to a set angle after first launch
*No longer able to move the upgrade screen around except by selecting an upgrade you need (which prevented me from getting the quest achievement, as my last 2 upgrades were outside of the starting view).
 "Curl Up and Fly!"){kind=icon}