Ladies and gentlemen, the mystery of the 2 pyromancy flames in 1 playthrough has been solved. Well, it has been for quite a while, but I finally got it to work for the first time. Here's what I did:

Picked pyromancer class, got first flame in the Asylum.
Saved Laurentius, no extra flame which is normal.
Levelled INT to 12 (the wiki's say only 11 is required)
After beating Quelaag I got myself bitten by the eggmonsters in the Demon Ruins and waited for my head to turn delicious.
After egged and all, I dropped my first flame in the hallway
Then talked to Eingyi to let me pass
Joined the covenant
Talked to Eingyi to get the his talk options
Selected talk
Got the second flame
Picked up the first flame I dropped moments earlier

On a sidenote; Aural Decoy = OP but hilarious. Makes creatures go full retard and I can't wait to try it out on Seath.