The feat Spell Perfection reads
Pick one spell which you have the ability to cast. Whenever you cast that spell you may apply any one metamagic feat you have to that spell without affecting its level or casting time, as long as the total modified level of the spell does not use a spell slot above 9th level. In addition, if you have other feats which allow you to apply a set numerical bonus to any aspect of this spell (such as Spell Focus, Spell Penetration, Weapon Focus [ray], and so on), double the bonus granted by that feat when applied to this spell.
Would the double bonus apply to the extra dice provided by Intensified Spell as long as your CL was high enough?
Normally the max is 5d6 with normal Intensify it would be 10d6. If Spell perfection would work on it it would be 15d6 max. That is if you have the CL to use all the dice.