The only problem I've occurred so far is when I'm in Besaid Village and I enter Wakka's hut (house/whatever) I am shown a black screen but the audio continues, I am unable to press any buttons or hotkeys when it's like this.

Something I did notice is that it changes from "Interlaced (field)" when I'm outside to "Progressive (field)" when I'm inside and that only occurs when I enter that specific hut. [See attached screenshots]

Things I've tried changing:

Round mode
Clamping Mode
Using synchronised MTGS
Disabling Speedhacks
Disable cheats
Graphics renderer (i.e. from hardware to software)
Resolution and scaling.

All to no avail so any help would be nice.

P.s. I was thinking of taking the iso from my game disk again but wasn't sure if that would make any difference.