I created another test to check if the issue was still there with 972.6.
In this scenario we have submarines and ships. The Los Angeles and the Perry are assigned to patrol, while the Virginia and the Burke are unassigned. This is what happens: the Los Angeles doesn't S&D on patrol, ever, while the Perry does it correctly. The Virginia is set to manual average speed but doesn't S&D along the trip, changing the speed again doesn't solve it. The Burke also has manual speed set and doesn't seem to S&D.
However, I could get it to work once for the Burke, it seems to depend on the order you check/unchek the boxes in and the current speed of the unit, but I can't reproduce it.
The problem is only there if you set a manual average speed, just checking the S&D box will make the unit work correctly, EXCEPT for submarines assigned on a patrol mission, they don't seem to S&D.
Thanks, that save helped indeed.
The problem was that the S&D-derived throttle commands were conflicting with the mission-derived throttle commands. Tweaked it so that the S&D commands take priority.
Fixed for the next update.