Hello my friend,
This gets a bit touchy.. You need to start the sub in ETO at either a Seaplane base..
Or in the water at the point where you want the mission to be..
The Mission builder will NOT ALLOW you to start on the gound in either the seaplanes or subs.
What you have to do after you finish building yiour mission is.
Open it up with notepad, or such progam, and set the Airspeed(speed) to 0.00, and the altitute( alt) to 0.00
By using Notepad..Then close the mission and it will go.
Something like this in the first waypoint line:
<Waypoint Type="turn" Speed="0.00" IsWarpable="n" Lat="N58*44'34.4313"" Lon="W10*19'17.7639"" Alt="0.00"/>
I hope this helps..