This is starting to drive me batty, but my AA count has been off for several weeks, and I always update with Magelo Update - unless it's offline (like tonight). I've gone through all my AA's several times, and it still comes up short ... currently shows me at 1214 and i'm at 1221. I know it's only 7 AA but it's buggin me and i'm OCD.
Some time back (around TBS release), SOE changed something in the EQ client so that their AA's total up different than magelo...after the patch that did it, I lost 2 aa's total wise in the EQ client and magelo has always shown those 2 earned. SOE back then admitted they had an error, and they fixed some of it, but they never got it totally fixed and I stopped sending in petitions cause they didn't seem to care.
Long and short of it is, the magelo sum is probably more accurate than the SOE one...its the one I go by.