OK. Exit the game and reboot. As far as I know, there is nothing else that you can do, but anything should be fine.
I am a software computer engineer, so my educated guess is that, much like a hell of a lot of other softwares, BG II 'eats' memory : it allocates bits of memory and 'forgets' to release them. So, after a while (one to several hours), the available memory in the system gets drastically low - and the only way to get it back is to reboot.
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