Supposedly (retroactively speaking) Kup has those implanted subroutines in his head but we don't know if Prowl's subroutines are influencing his actions during AHM 1-12 or not.
Personally, I think that Prowl's subroutines have not been made active as of yet as Kup was not acting 'Prowl like' during AHM issues 1-12. It's possible that given the Autobot's near defeat during AHM, Prowl placed his agenda on hold until the Autobots get an upper hand or simply lost the means to activate them while exiled on Cybertron.