I logged into Puzzle Pirates again last night. Watch out for this gotcha (at least on Gutsy Ubuntu Linux): Resizing Puzzle Pirates to the size of your desktop paints you into a corner. The game lacks a full-screen option, and between its menu bar and the Ubuntu tool bars the stuff at the bottom of the game's window gets pushed off the screen - including the options button! I suppose I could have tracked down the config file and fixed it there, but turning on autohide for Ubuntu's toolbars brought enough of the window's bottom back onscreen to click on the options button. Moral of the story? Make Puzzle Pirates's window one size less than your desktop's height.
As I had planned, I abandoned the pirate crew I had foolishly joined the previous night and rejoined the Navy. I set about learning the various puzzle games, and found this nearly as frustrating as being on a real crew. Some of the games - it seemed to be the single-player ones - had a tutorial tab explaining how to play, but none of the multiplayer games I tried did.
What I would have found useful - but couldn't locate within the game - is some sort of centralized collection of puzzle instructions, the sort of thing one would find in a game manual. I did find it later in YPPedia on the game's website, but would have appreciated having the same information available in-game.