i'd like if someone would analyze his zip, as i'm having a very similar issue. i've gotten FML to work, but now even though my mods are in the mods folder (i dont have any coremods) when the launcher downloads the zip, it doesnt get the mods out of the mods folder. (or something like that, i'm not sure)
i fixed my issue today, my issue was i didnt have a coremods folder (because i didnt have any coremods) apparently it still needs the folder. sorry i can't be of much help to you though.