The site category widget and the site category page only show about half of the sites associated with the chosen category. I have set the "Number of Sites to show" and "sites per page" options to "all" or a high number. In the widget backend it says the number 27 between brackets after the category name in the "Site Category" dropdown. But in the "Network Admin/Sites" overview I count 55 sites in that category. I tried to open the site category setting page of one missing blog and it shows the right category. I saved again (without changing any setting) and then it appeared in the widget and site category page. So it seems I found a workaround, but this costs me double the work and I can never be sure all blogs really show up in the site category widget and site category page. I have also not tested the workaround works for every missing site.