Ahoy matey, welcome to the forums <img src="style_emoticons/<#EMO_DIR#>/smile.gif" style="vertical-align:middle" emoid="

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You must be referring to the situation when you leave Oxbay when the invasion starts. The fort is now french, so naturally they will fire at you! So... (think capt. Blood here or maybe some other sneaky pirate)... the solution is to raise a neutral flag!
Before you get onto your ship to sail out...
Go to your F2 menu, Relationships, and raise a Portuguese flag (they are friends with everyone). Or raise a French flag - that should also work... just don't forget to raise your english flag again when you are out of there (just go into the 3d mode again in the middle of the sea, raise a different flag via the F2-relationships, and then go back to map sailing.)
Have one on me in the next port <img src="style_emoticons/<#EMO_DIR#>/biggrin.gif" style="vertical-align:middle" emoid="

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<img src="style_emoticons/<#EMO_DIR#>/par-ty.gif" style="vertical-align:middle" emoid="

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