I was doing the Aegis of Life quest on my cleric alt, I got the items and ally faction, I turned the items in and the NPC ate them even though I had enough faction.
Here is a link for the quest:
http://everquest.allakhazam.com/db/quest.html?quest=454
And a Screenshot of my faction and turn in time stamped:
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Notice he cons ally and you only need high warmly to do the quest. Also notice he said "you have not yet proven yourself" meaning I did not have high enough faction, but my faction is maxxed so something is set incorrectly.