Why does Beamer's table of contents items link to the second slide in a section?

This was due to a bug in beamer, which only shows up with some viewers. The problem comes down to where the target is located for page links. The behaviour was to place this in a footer, which is not really correct. The code has now been updated to place the link in the 'correct' place during shipout, and this fix will appear in the upcoming v3.28 update to CTAN.

As you already explained there is a workaround, until the beamer package is updated with the bug fix Joseph Wright mentions. By putting your PDF viewer in Single Page mode you are able to correct this behavior, which was also present in Adobe Acrobat 11 (and probably <11 as well). The simplest way, that doesn't require the viewer to select this view mode manually, is to add the pdfpagelayout option to your hyperref options, like so:

\documentclass[hyperref={pdfpagelayout=SinglePage}]{beamer}

Note that the hyperref options must be in curly brackets and supplied to the hyperref option of the beamer class. This is due to beamer's dependency on the hyperref package, which it loads for you automatically.

I have found a solution, or maybe a workaround? The described problem appeared when viewing slides in "continuous" mode. If I disable this so that the viewer jumps from slide to slide instead of scrolling across them, clicking links does take me to the right slide. This goes for both Evince and Okular.