Well, I'm assuming that your machine is either off or sleeping at night, which is when OS X usually runs little scripts that take care of the log files -- they either get deleted, cleaned, moved or modified in some way, and those scripts keep the log files nice and clean and small.
Use Cocktail to run the cron scripts under System > Scripts (running all of them the first time could take a few minutes).
Oh, and JFS doesn't have anything to do with the log files. Even if you had never turned JFS on, the logs would still have been mighty large.