OK.. here we are! ... I figured out my sub has TWO battery recharge cycles! (at least it looks like).
And this might mess up the speed management.
Take a look at the message box on the lower right of my screenshot:
##EDIT##
I just found out that when the Trevally Automated Script (patrol) orders to dive for a hydro sweep and sets "All Stop", the speed under water doesn't drop below 2.6kt
I then used the hydrophone to listen if the screw is still turning but it IS NOT! All quiet but still holding the speed at 2.6kt
Then I pressed the "Standard Propulsion" button at the engineers menu. The voice and log gave me a "Secure Recharging Battery" "Standard Propulsion" ... which is funny, because i was at 30m for 2 minutes and the diesel engines should be turned off minutes ago.
After I ordered "Standard Propulsion" the boat immediately lost speed.