I hope no-one minds me replying to this old thread, but a player in a game I'm running will be using Magic Jar in the future and I'm researching into this now.
I've actually answered this question for -my- game, obviously that doesn't mean that it suits everyones game but I felt like sharing my thoughts, for those that might be interested.
Firstly, why does the 'personal' category of spells exist in the first place (in flavour terms). I assume it's that the spells power is maintained by the caster in some way, a pretty standard concept in fantasy games that involve magic. So casting it on yourself works because it then feeds off of your magical talent in some way, whereas casting it on the fighter will fail because it will instantly run out of energy and collapse.
Secondly, what do we target when we target a spell at someone? Their body or their mind, not their soul (except with specific spells that state otherwise).
So if you have comprehend languages and mage armour up when you cast spell jar, the mage armour keeps running on your original body and the comprehend languages fails as there is no magic to sustain it. Likewise, if you cast them in another non-caster body and then return back to the gem. This means that you can't use magic jar to give people spells they couldn't normally get and there is a consistent in-story reason as to why that is.
As for permanent spells. I'd argue that permanency keeps the spell running but it only works while the same kind of caster (arcane/divine) is using the body. So jump into the body of your fighter and make comprehend languages permanent and it seems to work, jump out and let the fighter return and the spell fails, kick him out of his body again and the spell comes back to life.
The only way around this being that a wizard could cast a personal arcane spell on a sorcerer's that lacked that spell, make it permanent and then have it work for the sorcerer... but then he could do that by buying a spell-page with the spell on it.
This means that all spells, unless specifically aimed at the soul, stay with the body - even mental ones. It simplifies things a great deal, reduces abuse and it's still fair, no-one could argue that it isn't a powerful or useful spell even when ruled as strictly as this.