PokerTracker/Account History - numbers don't match up?

[shant]

Hi guys,

So the other night I played on Empire at about 3am after drinking a lot of whiskey. Anyway, Party was doing maintenance and started closing tables. So I went to sleep. The next morning I wanted to see how I did. I ran the one day filter on PT and it said I won 85.50. However, I checked my Empire account history, subtracted final total from 3/10 and 3/9 and that said I had only won 53.50.

Why would there be such a large difference? Is the PT number with rake not factored in? Also, sometimes while in a hand, my connection will have a problem, and I fear that PT isn't getting a complete HH. Is it that or just the rake thing, or is it something I'm missing?