I'm not sure there's an easy answer to this question.
How do you motivate players to use jobs? It largely depends. When you're dealing with Completionists, just the act of having the other jobs is typically enough to get them to use it. For everyone else... that motivation is going to vary.
Just based on your short description here, my immediate thought to "fixing" your system is as follows:
1. Add a "secondary" Point System for each Job. Your Job Points allow you to learn every skill for every job, even if you haven't played them. However, a secondary point system that would only go up for the job you are playing would give stat boosts, passives, or even something like a "Finisher" for the job. The "finisher" would basically just be your "Limit Break" skill, and it could only be used once the job was "maxed out", and only on the job you're playing as (so a Knight's finisher couldn't be used if you were a Thief).
2. If you want players to pick a job and stick to it for long periods of time, just make it fun to continue using. If a job is "one note", then it's only good for that "one note". But, if it has a bit of versatility, it can be useful in many different situations. Maybe give the jobs a gimmick. Final Fantasy 6 had "gimmicks" on their characters and those gimmicks were pretty fun. I still like Setzers "slot machine", and I love Locke's "Mug". I also loved "Sword Tech" from Cyan or even "Runic" from Celes. A distinct reason to keep playing the class, like it has a fun mechanic to use, is a way to keep players using it.
3. If you wanted players to swap jobs decently frequently, then I would just suggest you tailor challenges to specific groups of jobs. Maybe this dungeon can't be tackled by mages, so you have to use all the melee classes here. Maybe this dungeon can't be tackled by anyone who uses weapons, so players have to use Monks and Wizards. Stuff like this would get players to try different things, and you could have fun with what limits you put in place. You could even have an "Eastern Themed" dungeon where only Samurai and Ninja can be used. The possibilities are near limitless. Only restricted by your imagination and ability to write convincing Lore reasons (or, ability to make players not care if your restrictions exist, because it's the type of game that just doesn't take itself that seriously).
Anyway, those were my initial thoughts on the subject. Not sure how helpful they are to you. Unfortunately, I don't have much of a description of your system to go on here to go more in-depth on the subject, and I also have no idea what specific things you're trying to accomplish with your Job System. Without knowing either, my reply is limited to this specific "knee-jerk" reply.