This happens to me sometimes when I'm trying to summon Ultimate End. In that case, I think there are just so many files to read out of the magic.lgp file that the game pauses for a second or two to get them all.
Are you playing from a maximum install or standard? It sounds like a standard since even basic spells are laggy. If that's the case you might want to enable direct disk access for your CD drive. I don't remember how to do that, but it fixed a horrible lag problem I was having with FFVIII back in the day.