@Nightcrawler: If I'd hazard a guess. Could it be the rendering filter at fault to that issue I've encountered?
I use hqx3 and I've read on some other emulators for other systems, that sometimes the rendering filter can cause issues like this on games.
Anyway, it is a minor issue as I've said and it fixes itself up if I cancel the selection by pressing B and having the menu "refresh" itself (by refresh I mean after pressing B and the game re-positions the selection to the attack option.
The way I trigger this glitch is by immediately moving the selected action from attack to sword arts as soon as possible on the very first battle after I go out of the wall and back onto the Atlantis island map.
And finding other factors to blame... could I have possibly triggered this glitchiness from the fact that I opted to "curse" (use foul language) on the segment where Plato asks you to pick out what to inscribe on the wall after the scenes with Epipha? Kinda like the game punishing me for inscribing the "F" word on the wall? LOL
Also regarding trying the game out on another emulator. I'm not really into having multiple emulators for playing games for a specific system and my personal choice for an SNES emulator has always been Snes9x. Anyway, you've tested for yourself that issue isn't occurring at your end so it's safe to say that this isn't entirely a game breaking thing that needs attending to. As I've also said, maybe the game just didn't like my use of foul language ROFL!