I honestly think it's got something to do with spellweave dmg...i mean i'm around 380 ilvl on my shaman and i did 50k+ (don't even have 2 piece bonus) on madness in LFR...however i switch to aoe fire totem, throw an earthquake before the bloods come and do the mana regen thingy which does aoe dmg and is instant, if they're not dead I also throw 1-2 chain lightnings.
Also maybe save elemental mastery for when DW arms (i think) are under 50% since the less hp they have the more dmg they take (notice the stacking debuff on them). Also use fire elemental only when you have some intelect procs (power torrent, lightweave if you're tailor, on use glove enchant if you're engi, volcanic potion if you're using etc, int from one-use trinket or max stacks on WoU trinket).
Depending on the dps in your group you can use fire elemental twice once in the beginning and second time on the head. Try these and see if you get any improvement.