Hi Hakuen!
Sorry for the alarm, I managed to find a simple solution.
It was the "Enemy emerged!" window being stuck on screen even as the battle commands are up. I just added a 60s wait before the next dialogue on the IF WIN/IF LOSE condition and sure enough, the window closes for some reason lol. Could be a minor compatibility glitch as well as i didnt encounter the same problem on a sample project.
Thanks again for the speedy reply! It's all good now :)
Thanks