I'm glad it's fixed. The reason it took so long before is that the stock game doesn't recognize 'refueling'. If you stop anywhere it assumes the patrol is over. Your boat is repaired, refueled and rearmed and your crew goes on leave.
SH3 Commander not only lets you refuel and rearm overnight without a delay, but if you set 'Days in Port' to Random you might be at your home base longer than a month, or, as happened with me in a Type IIa after going home with all my torpedoes, five days for a complete turnaround.