@Pythos, I think you are using a mod that uses a different crewmembers.upc.
you can use one from a playable ship mod if one was provided.
@Sophont, if you want to, open up the tower.dat in S3D and look for O01 and O02, those, metinks are the periscope nodes, adjust the Y value up, but not much, and that should fix your problem