I could not reproduce the issue with Chrome 12.0.742.91.

If you're using Flash content in fullscreen, chances are this is the root of the problem as it may be executed in a separate process that doesn't identify as Chrome. This in turn would trigger Remote Buddy to switch away from the Google Chrome Behaviour to another Behaviour - which may not have anything mapped for the buttons you press - and you'll get a standard mac error sound.

You could possibly get around this by telling Remote Buddy to make the selection of this particular Behaviour sticky - until you explicitly deactivate it. You can do this via AppleScript to make the current Behaviour (yours) "stick":

-- cut -- 
tell application "Remote Buddy" 
behaviourcore accessor "setSticky" with stickyValue 
end tell 
-- cut --

Another possibility would be that when you send the keystroke, the respective window (from Flash and/or Chrome) doesn't have keyboard focus and that the keystroke you send creates the standard mac error sound. For this, I can't offer a solution, sorry.

Best regards, 
Felix Schwarz