The main issue in the past with Commander was if it was installed in any of the Program Files folders, and that would cause issues with settings not taking effect. But if you've avoided those then that shouldn't present many problems. Do all other Commander related settings work as expected when you start the campaign, like U-boat type/number, patrol grid, career options in the preferences etc?
Also, and apologies if this seems like a silly question, but are you actually launching into the game via the SH3 Commander interface, which is needed for the settings to take effect? If so and all other aspects are working properly I can't really think of much else at the present for why only the start date would be wrong. Maybe try compatibility settings on SH3Cmdr.exe (Windows 7) and run as Administrator if not already. Best I've got for now I'm afraid. Hope to see you get it sorted.
