There's quite some text for section 1 and apparently the line height for the section header is too high, so the text on column two is not aligned with column one until there's a new paragraph to correct this. Easiest way is to lower the header a bit, but I couldn't find info on that.
Sorry. If you fill in the text below the section with a lipsum to fill a whole page, the second column is not aligned with the first column text because \section{} uses about 3.5 lines, and not 3 or 4. After a paragraph in the second column half a line is added by LaTeX automatically, but before that it just looks crap.
You could try fiddling with the \titlespacing*{\section}... command from the titlesec package, but in my experience, it's usually not possible to have your columns always have aligned lines of text, at least not if you're also doing things like widow/orphan control, consisting spacing for section titles, etc.-- throw in an equation or diagram or two and all hope is lost.