I made a new install to test this and decided to play the standard storyline. All went well until it was time to sail away. I don't know if this is related to PirateKK's code or not, but some of the ships had missing flags. A fastmerchantman had no flags or pennants while the Aurora class frigate had pennants but no flags. The biggest ship had no flag on the flagpole. The Kreyser class frigate looked ok as well as some luggers and barques.