A question came up in a game earlier about whether the Mystic Theurge could use his Lesser Metamagic Rod of Empower Spell to Empower an Intensified Fireball he was casting from one of his 4th level spell slots. Our thought at the table was that it wouldn't work since Intensified Fireball counts as a 4th level spell. Is that the correct ruling?
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What matter when you use the rods is the spell slot used by the spell.
There is a recent FAQ about that:
Metamagic: At what spell level does the spell count for concentration DCs, magus spell recall, or a pearl of power?The spell counts as the level of the spell slot necessary to cast it.
For example, an empowered burning hands uses a 3rd-level spell slot, counts as a 3rd-level spell for making concentration checks, counts as a 3rd-level spell for a magus's spell recall or a pearl of power.
In general, use the (normal, lower) spell level or the (higher) spell slot level, whichever is more of a disadvantage for the caster. The advantages of the metamagic feat are spelled out in the Benefits section of the feat, and the increased spell slot level is a disadvantage.
Heighten Spell is really the only metamagic feat that makes using a higher-level spell slot an advantage instead of a disadvantage.
—Pathfinder Design Team, 10/18/13
Ok, there's no direct information on metamagic rods in there, but I think we can infer how it should work based on the parts you bolded and the interaction with Pearl or Power. Thanks!
Yeah, the spell counts as the slot it is cast from.
So that 4th level spell would need a normal rod (not a lesser) of Empower to function.