The 'Auto Surface,Submerge,Attack' orders in the crew management screen have been buggy since release. These have never been fixed, in fact I don't think they can be.
We have all got used to not using them as they will, 90% of the time cause you to CTD.
Do it the hard way, surface the boat and then move your crew manually.
There are shortcuts for moving your crew around. IIRC, left click on a compartment/station then right click on the rest quarters or crew member and they/he will be moved instantly. (I think it's that way round
) But there's always the drag & drop method.