I’m having the exact same problem. There seems to be an extra space or two in the thumbnail grid. See the screenshot. Since the changelog for 1.9.13 said you were doing some centering, I thought maybe the CSS to do this was part of the issue, so I reverted to 1.9.12, 1.9.11, and 1.9.10, but the issue remained. This issue appeared after a few new images were added to the gallery, so I’m not really sure at what version the issue first made its debut.
I also switched to the Twenty Twelve theme, deactivated all other plugins, and used a different browser with a clean cache. The issue remained. See the screenshot. I’m using the current version, WordPress 3.5.2.
I was able to manually sort to make the extra spaces go away. My technique was to swap the two thumbnails immediately before the extra space(s). On a different gallery I re-genned the thumbnails to fix it. For now it’s not showing the extra spaces, but here’s the relevant page on the live site. Of course, now we can’t order the images how we want, and now we’ll have to check after uploading new images. Essentially the plugin is broken.
This is a super huge bummer, because I’ve confidently used this plugin for years on many sites without ever seeing this issue.
Thanks,
-Brett