I looked a little bit more precisely at it, the thumbnails in the widget are the same size but are overlaying. That means they look different, because one thumbnail is laying over its neighbour-thumbnail. Therefore it looks like different sizes. It wasn’t like this before updating.
After updating to the newest version of FLAGallery thumbnails in FLAGallery widget don’t look nice any longer, they seem to have different sizes in the frontend now, although width and height are given in the backend. Is it possible to change back the plugin to an older version?
Fancybox works! Thanks.
I found the problem myself, it was the plugin Thickbox which prevented it from showing up. I need Thickbox for my video plugin as FLAGallery unfortunately doesn’t show vimeo videos.