Thanks for the reports! We've implemented a hotfix to correct this issue and ensure that eligible Horde players are able to receive reputation with Bilgewater Cartel when completing Lunar Festival coin quests.

The hotfix requires a realm restart, so everything should be resolved after tomorrow's scheduled realm maintenance: http://us.battle.net/wow/en/forum/topic/1921699337

*If your realm has undergone a restart since Friday, the fix should already be in effect.

(...)To my knowledge, Alliance coin quests are currently granting the proper amount of Gilneas reputation when completed. Let me talk with our designers, though, to see if there's a cap at which reputation from those quests is no longer provided. It's certainly possible, but I want to be certain before I say one way or another.

This seems to be a bit different than what was happening with the Horde coin quests, by the way. The issue there was that the quests weren't providing reputation with Bilgewater Cartel at all, regardless of a player's faction standing.