You end your patrols at the "Home Port", such as if you leave from Pearl Harbor, you return to Pearl Harbor, unless ordered elsewhere. In either case, if you look at the Navigaion Map while in your boat, "Home" is designated by a tilted anchor, while re-fit ports are shown with straight vertical anchors. However, there are time periods in the game where a "Home Port" won't show on the map for a few days, such as during the early war period when the Asiatic boats are moved from Manila to Surabaya to Fremantle.
In the meantime, do you happen to know which version of the game you have is? Does it say "Gold" on it? Does it have Uboats in it? Is it a disk or a download? When you re-install the game, do not install it in the default "C:\Program Files (x86)" folder, which is a Windows protected folder. Myself, I have taken the path line, and just deleted that windows portion of the path, and used "C:\Ubisoft\..." as the install path (keep the "Silent Hunter Wolves of the Pacific" also...).
btw - "Welcome to SubSim!