I unticked 2 flags for Latios(I got αS) and Delta Episode started again...

[Gostas]

I unticked the two flags (Capture and Defeat) for Latios because I wanted to catch it again. I was at Battle Maison at that time. To my surprise, when I went out of Battle Maison, there were 2 Wally(s) standing by my statue(50 wins for Super Single). I laughed it off and continued.

When I went back to Petalburg, the cutscene where you see the Beautyflies with May appears. I'm like "WTF?". That's not all. An invisible person doesn't let me go upstairs in the Museum(I got all the Contest badges) and the Delta Episode started.

I tried to re-play the story(the character was talking to invisible NPCs and was walking through walls lol) but when I went to Sky Pillar and the Dragon Girl was telling me "Rayquaza is trying to store some power" or sht like that, nothing happens. There is no Rayquaza in front of me. I tried hitting "A" blindly in hope to find Rayquaza but nothing happened. I even reseted the Deoxys flag but thr Delta episode and the cutscenes started from the beginning! There was even Deoxy's Triangle alongside the Dragon Girl. It's pretty funny and I can laugh it off, but I want my game to be perfect and get rid of the problem that I created.

I am running latest version 10.3.0-28E and I have the latest *hax stuff so I can backup and edit my save file. My αS is @ version 1.4

Here are two images:

http://i.imgur.com/oMBDmVQ.jpg

http://i.imgur.com/485prLZ.jpg

And all I did was reset the 2 flags for LatiOs (Defeat & Capture) FFS

Edit: i had tried resetting the two flags (Defeat & Capture) for Kyurem back with TubeHax and I had caught 2 (One Modest and one Adamant) successfully without interrupting my story with those lame bugs...

[Gostas]

Well, gg wp ez I got another Rayquaza and Deoxys.

[DracoMilesX]

I noticed this too with other things in the latest version (The one that's stickied 20th dec?). That sometimes story shortcuts are replayed.

Haven't checked yet with the latest update.