So, this toon did the Shadow Vault dailies once our twice a long time ago. Then Vile and the others at the Vault just stopped offering any quests. I'm exalted with them, but was never able to get those quests again. I petitioned a GM once, but got the standard "can't give hints" answer, which seems a bit wrong. At the time I wondered if it was just a matter of the GM thinking I was asking how to create the Shadow Vault, which is definitely not the case (did that while leveling, back in early Wrath).

Is there a known bug that would prevent someone from getting these dailies or am I just missing something as the GM implied?

If you did a faction change, you need to repeat the short quest chain that opens the shadow-vault area for your new faction.

You don't lose Ebon Blade faction - but that area isn't open again till the new chain is complete.