Dot Hack Quarantine Anti-Piracy??

Playing through Quarantine and I made it to the 2nd to last dungeon. Go down to the boss room, and it skips a cut scene
and teleports me to an empty boss room (2nd Cubia fight).

Is this a form of copy protection or am I just really unlucky? If this is a form of copy-protection do you guys know where the patch is?
I can't seem to find one anywhere.

I don't think it's an anti piracy trick because they rarely work like that (they typically try to stop the game from booting in the first place). Either you're unlucky, or you're using a speed hack that messes with the game too hard for that moment. Sometimes a speed hack works fine most of the game then all of a sudden something happens that the speed hack alters to go faster and it doesn't work as expected (had that problem during the final boss of Kingdom Hearts 2 before). If you have a save from before that (a real one not a save state preferably) try disabling any speed hack you have and try again. The game has low requirements anyways.