So everything is going fine, I'm playing Pirate Gold, plundering cities. Then I enter a naval battle and regardless of the outcome, I always lose all my cannon and gold for no good reason. What gives?

Got the same problem here.

Just started a new game, captured a few ships and sold them. At the beginning of the next battle i have lost all my cannons and after the battle also nearly all my gold is gone regardless of the outcome.

Is this at the very beginning of the game? I know that if you fail the copy protection (guessing the correct name the first time you encounter a pirate), you lose your guns, your crew is unhappy and I think your ship is damaged, too - and you possibly lose your gold as well, I don't rightly remember.