Hypersmurf said:
"Spells cast on other creatures, objects, or locations (not on you) are vulnerable to dispel magic as normal."
My reading of that is that the original spell is the one you're dispelling. All Permanency has done is change the duration of that spell. So you'd use the caster level of the original spell for determining the dispel DC.
Be a little careful here. The quote about the vulnerability to dispel magic seems to be in reference to the fact that in regards to personal permanencies...
"This application of permanency can be dispelled only by a caster of greater level than the character was when the character cast the spell."
So, if I cast a permanent darkvision on myself as a 10th level wizard, only spellcasters 11th level or up can even attempt to dispel it. If I cast it on the party's Fighter, then any spell caster can attempt to dispel it.
Personally, I'd treat the permanent spells in a manner similar to magic items. That is, the effects are suppressed for a number of rounds. Though, you're reasoning certainly makes sense, and my ruling would certainly be debatable.
I'd rule it that way, mainly because it'd kind of stink to have to burn the experience points every other week, to recast the permanencies after you've been dispelled.
Mord's Disjunction, however, would absolutely end any permanencies.