As written there are two main issues with Mage's Disjunction.
1. It is not completely clear if the caster's effects and items are immune, or only the items. I am assuming the former because that reflects older versions of the spell without the ambiguous wording.
2. The spell has been given a duration, RAW this means that the spell would be a cloud that stays for minutes per level. I'm pretty sure it's intended to be an instantaneous flash of disjunction and then a duration on the following suppression. By wanting to make minimal changes to the text of 3.5 spells, they accidentally introduced this error. I'm pretty sure they meant it to be an instantaneous flash because otherwise the spell would have text describing what happens if you start/end your turn in it, and what happens if you enter the effect.
In light of those two issues and the obviously intended interpretation of the ambiguities, I have rewritten Mage's Disjunction for use in my group to remove the ambiguities and still retain all of the intended functionality.
School abjuration; Level sorcerer/wizard 9; Domain magic 9
CASTING
Casting Time 1 standard action
Components V
EFFECT
Range close (25 ft. + 5 ft./2 levels)
Area all magical effects and magic items within a 40-ft.-radius burst, or one magic item (see text)
Duration instantaneous (see text)
Saving Throw Will negates (object); Spell Resistance no
DESCRIPTION
All magical effects and magic items within the radius of the spell, are disjoined. That is, spells and spell-like effects are unraveled and destroyed completely (ending the effect as a dispel magic spell does), and each permanent magic item must make a successful Will save or be turned into a normal item for the 1 minute per caster level. An item in a creature's possession uses its own Will save bonus or its possessor's Will save bonus, whichever is higher. If an item's saving throw results in a natural 1 on the die, the item is destroyed instead of being suppressed. Magical effects on, or magic items carried by or touched by the caster are immune to this spell's effect.
You also have a 1% chance per caster level of destroying an antimagic field. If the antimagic field survives the disjunction, no items within it are disjoined.
You can also use this spell to target a single item. The item gets a Will save at a -5 penalty to avoid being permanently destroyed. Even artifacts are subject to mage's disjunction, though there is only a 1% chance per caster level of actually affecting such powerful items. If successful, the artifact's power unravels, and it is destroyed (with no save). If an artifact is destroyed, you must make a DC 25 Will save or permanently lose all spellcasting abilities. These abilities cannot be recovered by mortal magic, not even miracle or wish. Destroying artifacts is a dangerous business, and it is 95% likely to attract the attention of some powerful being who has an interest in or connection with the device.