Someone must have recognized Flynn and ratted him out! A bunch of Irontide thugs dragged him off to the Ring of Booty for a "special audience" with Captain Harlan Sweete.
Flynn doesn't like to talk about this, but he used to captain his own crew. With Harlan as his First Mate.
The two had a falling out after a messy job and Flynn lost all taste for freebooting. Just disappeared one day.
Harlan took the nastiest of the crew and formed the Irontide Raiders.
In other words; it's personal.