ok, other people on the internet have come across this glitch, and it's bad news.
1) If you saved AFTER finding out the floor "did nothing", your save file is dead and you're completely stuck there.
2) If you have a save PRIOR to ever attempting the puzzle, there's a chance you can retry it and move on.
Apparently it's an issue with the way the game loads cutscenes, and completely forgets to load this particular one.
Have you tried leaving the Pirate Homeworld completely, visit another planet, then comeback to the Homeworld and see if the game makes the proper change?