Is this happening directly after you have been transferred?
Are you actually in St.Nazare? Sounds as if you are at a friendly port and not in your home port. Upgrades are disabled if this is the case.
My suggestion is to conduct a patrol and if not playing at 100%, just load the patrol and sail out of port range and then press escape and choose 'Return to Base'.
I don't think you are in the base you think you are.
Edit - Just re-read your post, by the looks of it, you are still in Kiel and your base has been changed. You need to get to St.Nazare anyway you choose.