As well as the "Ask Question" button being in a different position on the meta (See this question), the entire "content" div is in a different position between sites. It's not much, but you can notice a difference on both sides of the div.
Also, the padding on the "Hot Meta Posts" is correct for both sites, although the background for the main site overlaps the padding, probably one of the reasons that the entire div is unaligned.
