If you don't have anything running in the foreground that may be doing it,
like Gary suggested, what is your command target set to?
The option to manually select DirectX or Standard keypresses has been removed from beta v1.5.12.7 onward. You could consider upgrading to the beta, though I doubt that's the cause of your issue.
One thing I'd like you to try before messing around with the command target is to run the following action:
Write '[Purple] Active Window: {ACTIVEWINDOWTITLE} from process {ACTIVEWINDOWPROCESSNAME}' to log
If you run this while you're using Star Citizen, and the window/process are not Star Citizen, that's likely the culprit.