Similar problem noted
I'm still playing an earlier version of GWX (just downloading 2.0 now).
I noted that after crash diving, then ordering a deeper depth on the guage while still in the crash dive, if you switch to silent running while in the dive, you will continue past the ordered depth (nearly imploded once due to not catching my actual depth until the final moments and taking emergency action to prevent my descent right past 300 m on what was supposed to be a 120 M dive).
After thinking about what might have caused this, I came to the conclusion that flooding your tanks fully (crash dive mode) followed by shutting down the pumps (silent running) meant that the diving officer could not put air into the tanks to stop the dive. Screw RPMs and control surfaces set for ascent could not overcome the added ballast as I saw it. Under these conditions, I would consistently sink uncontrolled until I a) secured from silent running, and b) combined RPMs with orders for shallower depth.
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