Just noticed this in 2.2 Essential; not sure if it was in earlier versions.
In Configuration -- Sales Tax:
If "Detailed Tax Display" is set to NO, the confirmation email shows the Subtotal and then, immediately, the Total. The Sales tax line is not listed separately, so the numbers don't appear to add up. (see no-tax-item.pdf)
When "Detailed Tax Display" is set to YES, the confirmation email shows the line for tax, but it doesn't show a Subtotal line. (see tax-item.pdf)
It would be better for the email to show a Subtotal after the purchases, then to add lines for the shipping and tax, and then show the Total with everything included -- exactly like the web display that you see if you click the order number in the confirmation email (web-display.pdf).