I just realized how the changes to Dispel Magic affect Permanency.
In 3.x, Permanency was generally a bad idea for PCs, because they were likely to get hit with a dispel that would end the spell, causing the XP to disappear.
Since Dispel Magic now stops after one spell (or a few for Greater Dispel Magic), the Permanent spell is likely to last for several levels, especially if cast just before leveling. Assuming the target normally has at least one long duration spell affecting them, Dispel Magic will probably either remove the other spell or completely fail. Only when the Dispel misses the other spell by the difference in levels with the Permanent spell go down.
I wonder if Jason et al actively thought about it, or if it's just a happy, unintended consequence.
In 3.x a dispel magic would only neutralized a permanent enchantment for a period of time. It would not destroy a permanency any more than walking through an anti-magic field would.
A dispel magic against a permanency would be the same as a dispel versus a magic item. It is only disjunction that you need to worry about. The disjunction will trash the permanency spell.
In 3.x, it made the other spell permanent. It didn't make the spell into a magic item, in which case you would be correct. In fact, the text of the spell even talks about how it can be dispelled.
This application of permanency [on a spell which can only be cast on yourself] can be dispelled only by a caster of higher level than you were when you cast the spell.
Spells cast on other creatures, objects, or locations (not on you) are vulnerable to dispel magic as normal.
Nowhere does it talk about suppressing the spell.
Agreed... it's just the spell's duration is made permanent. It isn't made a part of you like from an Item creation feat.
Such permanent effects are subject to being dispelled.
In 3.5 that was unfortunate, concidering the xp expenditure put into it. But now with it being a GP expenditure, you can tend to afford the effects loss easier.