When looking at any module's category page, there are 2 boxes: one titled "Common Categories" and one titled "All Categories." Oddly, not all categories are listed in "All Categories."
See the following pages on demo.boonex.com for this error:
As you can see, not ALL categories are listed in the box titled "All Categories" - the easiest way to see this is that the "Common Categories" section has categories that aren't listed in "All." You can also see that it is failing when you look through each upload in the module section and see that there are categories missing. Or look directly at what is listed in "All Categories" directly under the Category section. For example, if you look at the Category page for photos (here-click the Photos submenu to see) you will see far more categories listed than on the category page on the Photo module (here). These pages should have identical lists of categories, they do not.
Although I've only listed some of the modules experiencing this error above for examples, this is a universal bug as all of the other modules w/ a Categories section also have this problem (i.e. articles, files, etc.).
How do I fix this bug?
P.S. I've uploaded screen shots of this bug so that you can see the bug directly.