What happened:
Game runs normally and smoothly on laptop.
Game suddenly becomes laggy (I was around chapter 4).
I thought it was because of my laptop so I copied the game and my save file to my desktop.
Game runs normally and smoothly on desktop.
Game suddenly becomes laggy again (I am at chapter 9).

What I mean by laggy:
Switching between pages in the inventory takes 1-1.5 seconds instead of instantly.
Leaving Yuidora and going to the world map loads twice as long.
During battle, whenever the character walks, it takes pauses on every square.

PS:
One time I was playing and the electricity went off. When I played again a pop up appeared,
it contained Japanese text and the word "Direct3d". I just clicked the 2nd option which is "no" if I remember correctly.
The pop up hasn't appeared in awhile. But I'm wondering if it has something to do with this lag.

UPDATE:
I solved the problem by reinstalling the game. I still don't know what triggers this problem but at least I solved it.