They were fully under control according to MK3 thru Armageddon, they only ever gained free will when their programming malfunctioned.

But in the new timeline...well, Cyrax acts controlled, but Sektor laughs and talks like he has a mind of his own, so who knows, maybe he planned to rebel all along and used his position as willing volunteer to change stuff before having it implanted

Maybe that's Sektor's malfunction. The being evil, i mean. In a take-over the world one way or another kind of way.

It seems in MK9 at least that Cyrax and Cybersub (until jax fixes the later) are under full control.

But Sektors personality doesn't seem to change much (plus he laughs a bit maniacally for an emotionless robot) so because of his blind loyalty and his willingness to be automated they allowed him to keep his humanity, where as Cyrax and Sub both resisted and where therefore put under full control.

Thats just how I see it anyways.

This sounds legitimate.