"The second spell doesn't count as being affected by a metamagic feat for the purpose of this benefit (that is, it doesn't entitle you to apply the metamagic feat to a spell you might cast in the following round)."
This seems to suggest that the second spell does count as being effected by a metamagic feat, but it doesn't count only for the purpose of this feat. (Otherwise we could chain this feat off itself endlessly.) I agree that metamagic efft & metamagic feat could be interpretted as two different meanings, but then the quote above would be rendered pointless if your interpretation of Residual Magic only applying a "metamagic effect" and not indeed a feat is correct.
While I agree with you X-Codes that your ruling seems the most likely, the wording is still fairly vague as to what spell level we could Heighten a spell to with a free heighten.
Hmm... I can somewhat see the other interpretation of "for the purpose of this benefit" now, although now it's an argument akin to the DWK one; nothing really clear going on. The position I put forward, however, is valid because the restriction on applying metamagic feats to spells is very clear: can't apply the same
feat twice. Most effects work within this structure using language like "empowered as though using the Empower Spell feat" for empower rods.
That said, heighten is pretty cut-and-dry if using this interpretation. You can't cast a heightened +6 fireball with a 9th-level slot, then residual magic that over to a second heightened +6 fireball to gain a 15th level fireball because both effects still carry heighten's hard cap of 9th-level spells, although you can do +3 and +3.
If you don't go by the interpretation I put forward, then I don't think could could cast a heightened +1 fireball and then residual magic it over to a heightened +6 fireball from a 3rd-level slot next round, because the effect you're trying to residual magic over is a heightened +1 spell.