Well my guess is. Either one of two possible outcomes.

Shinnok tampered with the Amulet so much that Sektor and Cyrax are still human and awaiting automation.

Or...

They are being used as Slaves for Quan Chi.

The only other thing I can think of is it has something to do with the time altercation other then that IRDK.

Unfortunately they'll probably kill Sektor, and maybe let Cyrax escape and eventually get reprogrammed. It sounds like it's all going to be explained in the comic though, and not really much in the game.