After hours of stealth and daring, I get my sub into the blue circle and depth set at less than 100 ft with speed of zero. Spec ops are supposed to deploy, but don't. Does time compression have to be off, or some other setting required for them to get out of my boat?

Have you explicitly loaded the Spec Ops when you were at you home base? Do you see their crest on the WEAPONS panel?

I have the latest version of the game and I do not have this problem.