Metamagic'd spells count as the slot used to cast them for metamagic rods.
The FAQ on metamagic spells and the levels they count for states:
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.
Since it'd be less beneficial for a caster to have the spell count as a higher spell level when using a metamagic rod, they count as the higher level spell.