I went to the Sonalyst Combat Page and looked at all the downloads for any problems with depth control. None was noted. Nemo is probably correct I would do a re-install and patch to 1.08, and install the SCXIIc mod which is outstanding. Another solution would be SubSim's Naval Combat Pack, which gives you SC patched, Fleet Command Patched, and 688i patched for about $20 plus shipping. Then mod SC with SCIIc and you got a deal.
Good luck,
Ron Banks, MMCM(SS), USN(Ret)