Chocobo_Fan, it sounds like you're playing an old version of the game. I'd suggest backing up your saved games, uninstalling, then downloading and installing the newest version of the game.
That's what I thought too, but I have version 1.810, activated and everything...
And, uh, how do I back up save games again? I don't think the previous trick for the .sol files works anymore, I did a search and nothing came up.
Edit: Ah, nevermind, I was using an old version somehow. The new one is definitely different. My savegames got eaten in the transition though, so I'll have to replay the intro to get back to the point I was before to confirm if the bugs are really gone or not.
Edit 2: Okay, the previous bugs are eliminated in the new version, but I found a new one: After completing Crypt 1, I'm teleported inside a wall in the library.
Edit 3: Also, the Blood Orb has magically disappeared from my inventory. Can I still get it back?
Edit 4: I also recruited Alissa, but she isn't at the hideout and no one seems to talk about her. The wiki says Rahel has some interaction with her, but all I can talk to her about is the usual stuff.