Yes, I experienced that myself. Once it happened to me completely randomly at the beginning of a patrol, and another time it happened to me immediately after a transfer to a new flotilla.
It seems to be happening very frequently whenever I try to start in the Black Sea or in the IO/PO though, and that's why I asked. I'm going to give it another few goes (currently at a count of four tries) and see if it'll remember to start me at Penang after I complete a patrol or something along those lines. It's a bit frustrating since I can't deploy to the IO or the PO until very late in the war and that doesn't give me much time to enjoy the atmosphere of the new operational area. 
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Winter Garden on the North Atlantic
Currently: U128 (Type IXC), U180 (Type IXD2), U198 (Type IXD2) operating in the I.O.
Previously: U48 (Type VIIB), U568 (Type VIIC) [Completed 1940-1945 career in Type VIIs, in the Atlantic]
Running: SH3 v1.4b w/ GWX 2.1
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