Here's something I'd like to bring up, don't know if anything can be done about it. I've been sailing out of Fremantle early in the war in a Sargo class sub. I recently was offered a new command of the USS Greenling. The thing is though I was transferred to Pearl but the patrol area I was given was still in the Java Sea. I've added a screenie to illustrate. One thing to note, I transferred to Midway to be closer to the action, so to speak.
I don't know for sure, but I think this has been a bug from the original stock game.