I have an answer. It is a display problem, Now that we can see exactly how much rep we have I recorded the amount of Rep before and after Baal and compared the difference to that was reported. This is what I got:

Before Baal 3178554
After Baal 3184441
Rep gained 5887

Reported amount 2676
Times 2 (buffs) 5352

Rep gained 5887
minus reported 5352
unaccounted 535

Expected From level 4 Loyalty card
2676 * .20 = 535

So it is all there.

I am closing the read