Yeah there can be an issue when your given a boat that shouldnt be at that base. In the Tambor there have been issues with everything from missing crew members, missing conns to bad saves. My last Tambor caused LOAD GAME FAILED message to appear on the screen after I had the upgraded fair weather bridge. Anything before could load but nothing after it.
It is just one of those issues players run into. I am sure more players would stumble across such issues with other games had they the life that Silent Hunter has. You do not find many games that have been continuously played by large numbers of people for 17 years straight like the versions of Silent Hunter.
The Admiralty chooses for you on the upgrade by checking off certain parameters in the files. A certain number of patrols with a certain level of success will activate upgrades.
You can manually change the UPC file to have the upgrades to your specific boat. I do not recall where you can manually change what boat your current career is on.
http://forums.ubi.com/showthread.php...upgrade-Forums
Have a read at this thread. Ducimus(a good modder) is talking about where he discovered the bug that causes these bad saves.