SOLVED: FF7 Major Bug with Boss Fights

I've started playing Final Fantasy VII a while back and I just reached the 68th floor of Shinra HQ... There, instead of facing 'Sample: H0512', I fought a single Zenene... Thinking it was just a simple bug, I defeated it and went on with the game... Later on, I discovered that (probably because of this bug) all Boss battles where rolled back... To make it clearer, I fought 'Sample: H0512' (when I enter the elevator with Aeris) when I was supposed to fight 'Hundred Gunner' and, later on, I had to face 'Hundred Gunner' instead of 'Rufus' (using just Cloud instead of my party, probably because the game thought I was fighting 'Rufus')... Finally, I didn't even encounter 'Motor Ball' after the motorcycle chase... Thus, I decided to ask for help in order to resolve this issue.

I use these modifications:
-Final Fantasy VII Remix [2.5.1]
-Aali's custom graphics driver [0.7.10b]
-Team Avalanche's GUI [2.0.8]

The scene look-up table inside Kernel.bin is screwed-up. In Proud Clod, open your scene.bin file, then select "File", then "Create scene.bin". It will tell you the scene look-up table is incorrect and will ask you if you want to fix this. Select "yes".

Alternatively, you can also use the Hojo utility, open your scene.bin, then choose "File" and "Update Kernel File".

Thanks, that fixed it!
By the way, is there a way to find out what caused this issue in the first place,  so that I'll be able to avoid it if it happens in the future...

Given that Aali's and Team Avalanche's modification do not touch kernel.bin and scene.bin, I would say the problem might have been caused by the Remix...

The Remix f*cks up the entire game. It is more than outdated.

Closed as solved.