The wording in Residual Magic states "you can apply any one metamagic feat from the first casting to the second. but without any change to the spell level."
If it doesn't change the spell level (as you quoted), then guess what?
Heighten does shit. And by shit, I mean "nothing", since all heighten does is change the spell level, and you can't do that.
This is one way to look at it, but this interpretation also means that DMM: Heighten doesn't do shit for the same reason.
Actually, there's a very clear answer in this which is explains Residual Magic's inherent awesomeness and inherent crappiness: You don't apply the metamagic feat to the second spell, you just apply the metamagic effect. The effect of the metamagic effect you are carrying over in your first example is that of a +6 to spell level ala Heighten Spell. Therefore, the second fireball is treated as a 9th-level spell cast from a 3rd-level slot, but it is not a Heightened Fireball.
By reading into this a little, I think you can actually use Residual Magic to effectively apply metamagic feats a second time when you use it. This is because you're simply carrying over the metamagic effect of the first spell, and then applying the feat to the second. The benefit granted by the Residual Magic feat
explicitly does not count as modifying the spell with a metamagic feat. As such, if you were to cast a CL 10 Empowered Fireball, you would deal 10d6*1.5 damage. If you then used Residual Magic to apply that effect to a second CL 10 Empowered Fireball, you would deal 10d6*2 damage. Sometimes, however, this still doesn't work. With the above example with Heighten spell, you can't adjust it any higher, it's already a 9th-level spell.