Pressing an F key in CS6 to call an action seems to cause the application to "double up" the action.
At first it was not obvious what was happening, as some shorter/simpler actions run so quickly that it just appeared to be a malfunction with various commands.
This happens with actions recorded in other versions, as well as those created directly in CS6. Running the action in button mode or by hitting the play button in the Actions pane do not cause this doubling. Only with F keys.
We've been able to work around this by inserting stops via the action menu.
You have the only known work-around. I have problems with the Default actions in CS6 not completing. I haven't figured out what to do with that yet.