My guess is that there are rounding errors that are causing the consistent inconsistent errors.
I have seen this in QuickBooks when more than one taxable item is in an order. Small rounding errors compound to make the total tax off by a few cents plus or minus. Because the amounts are relatively insignificant, I've never had a question about it. Heck, even if you use nothing but supplied paper tax tables, the amount owed the state is calculated on the total period taxable sales. When you add up all of the collected tax, there is most likely a small difference.
If you are really concerned, I would put in a ticket to tech support.