I recommend you train yourself to use Enter instead.

I hope your Enter key still works ;)

I normally use "Z" to confirm, and "X" to cancel option/access menu. IMO, much easier access since you don't get interrupted while moving just to push "Enter", or having to go all the way to push "Esc" to go to menu. You could also use the spacebar if you're not interested on my method.

Also, I think you may have to reboot your computer;these are common issues that happen once in a while when it's been on for too long and is being used way too much. I remember testing a project, and my character for no reason (I found no events causing this) just kept on walking left automatically at the field screen. I restarted my computer, and Rm2k3 stopped doing that.