Wait, so after beating the final boss again it corrected itself? I'm not even sure if I have the glitch, but can you check if you beat Sora's 5th Cite De Las Cloches special portal??? For some reason it isn't appearing when the forecast says it should but all my other special portals thus far have been fine.
I have to correct this a bit. Yes it seems the Bug does not care about Sora and Rikus Position, so actually it worked out somehow I could finish two Special Portals which were for Sora, then after that, the Game does not know Soras Portals anymore.
So it's the Semi-glitch which was named once in the other thread that occured.
If I am lucky and finish the game 6 times, maybe then the game will finally work normally.