Could be the save file. I've found another problem, though, one that's even present in the patch that Subtraction shared. Maybe if we can fix it, it'll fix the scrambling problem you're having too.
The draw index does not reset, but the cursor index does. This means if you're scrolled to the bottom, pick a skill, and then try to pick another skill, the text that displays doesn't line up with what it represents (so Fight is actually Empty, Magic is actually Fight, Item is actually Magic, and so on). I think we need to find a way to reset it, that might solve both problems at once. I'm going to take a look through the ASM again, see if I missed something.
The draw index does not reset, but the cursor index does. This means if you're scrolled to the bottom, pick a skill, and then try to pick another skill, the text that displays doesn't line up with what it represents (so Fight is actually Empty, Magic is actually Fight, Item is actually Magic, and so on). I think we need to find a way to reset it, that might solve both problems at once. I'm going to take a look through the ASM again, see if I missed something.