If I had to make a guess, I would say it's because we're not using the same font and the same font size.

It's much better and it fixed other alignment issues too.

Other issues I noticed:
The right border of the the separation/space between entries is not really aligned with the same border on the entry box.
The navigation items (Recent Entrie, Archive, etc.) are not vertically aligned. The page title is, though.
On the Month page, the month selector/navigation element is half outside the month box and the previous and next entries are above and below it instead of on the left/on the right (unless it's on purpose?).