Check MQ change from about a year or 2 ago. Truespirit faction started getting reset when a shm finished their epic. Check it out on the crucible forum as I am just a guy who heard some stuff~
I just did the shammy MQ maybe 2 or 3 months ago and faction was still maxed, but I do remember something about people having problems some time ago with it.
I think it only effected shm who finished their epics after the patch about 18 months ago or so. Shaman who were already done with it still had max faction and can MQ them.
Of course someone could repeat one of the easier parts over and over until faction is maxed if they wanted to MQ with low faction.