Another reason this can happen is when you install a mod which changes the flottillas locations, and then load a previous save game. The game gets confused as your save game says your at base x flotilla y, yet the changed flottilla file says flottilla y is suppost to be at base z. So it will attempt to have you transfered to flottilla you belong to according to your save file and get you to move to its "new" location.
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