I dunno if it's related, but had this problem when I transferred to Wilhelmshaven from Kiel in late 1939.
I did this transfer on the stock game then installed GWX before starting my first patrol from that base. Because GWX didn't like my new location (historically inaccurate), I too got the message about my base being changed and then deposited where the greenwich meridian and equator cross (KM grid FG28). I had to reload my game from the end of the last patrol before I applied to change and it works.
tl;dr - From the experience I had, it sounds like it could be a conflict between start location and availability.
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