We've had something similar happening lately.. On certain mobs it seems that we get a different readout within the raid itself..
Like on nightbane today, Hunter pulling Nightbane off MT with a 44% difference between the two. Doesnt make sense.
Nightbane has been a serious issue for us lately, locks/spriest and hunters all yanking aggro when they are well below the threshold on Omen. As well as soulshatter resists not showing in Omen (omen reports the threat reduction but the threat wasn't lowered due to a resist)