I found 2 modules that I want to play with my drupal. Those are Lightbox v2 and Thickbox. I installed both module at the same time and then, I ran into the problem of using contemplate to change some template setting. I couldn't create template because the box that shows "Affect Body/Teaser output" didn't show up. It showed only what I already have done. But not what I plan to make a new one. (That included if I unchecked that "Affect Body/Teaser output". After save, it was gone.)
Since I've tried thickbox first and because thickbox seems to have something to do with template compare to lightbox that can just add "REL" command in the A HREF tag. I thought that Thickbox caused this problem. I tried to uninstall it but the problem was still there.
Later, I tried to uninstall Lightbox V2 and it came to work normal. So, the source of the problem is LightboxV2, not Thickbox. BTW, the Thickbox module I've used is 5.x-1.x-dev (06-Apr-2007) and LightboxV2 module is 5.x-1.x-dev (30-Apr-07).
UPDATE : Newer Version of Lightbox (Version 1.1) already fixed the problem above.