IIRC this may be an issue with Commander and/or the game not knowing where to place you on the map at the start of a new patrol, because the base change is not being handled properly. So it puts you in a "default" location of 0° latitude and 0° longitude, which is off the coast of Africa.
Sorry I can't remember all the details about what exactly causes it and how to fix it - but somebody here will, because it's happened to other players and come up for discussion before.
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