There are plenty of things you can do, Stig. Giving and taking away Counties is no small thing. If anything, Jan's lack of a Franconian county was one of the things that made him flee to Outremer. Furthermore, you can give your Electors command of your Household Armies (now that there will be 2). This will give them battles to fight, which is an incentive for most people. At the same time, you can strip an Elector of command of an Army, thereby denying him battles as a punishment. This doesn't even take into account the biggest incentive of all: making someone the heir to the Duchy. Many players will do almost anything their Duke says if they believe it will lead to them inheriting the title.

If a Duke has a very serious problem with an Elector that cannot be solved any other way, you can always make an appeal to the Chancellor to have him help you. The Chancellor can go so far as to make sure the person finds himself in an un-winnable battle, facing disgrace or even death. This is another reason to be on good terms with the ruling Chancellor, as it gives you access to options you would not otherwise have. It is perfectly reasonable for the 'factions' that support the Chancellor to receive preferrential treatment and the occassional favor in-game. Remember: there is essentially nothing that the Chancellor cannot do. You may have to negotiate for what you want, but unless you have really angered the Chancellor, I suspect he would be willing to aid you in some manner.