I noticed this issue with Blog, Calendar, and Gallery so far, I don't have Filebase to test with currently.
1) Create top categories, sub categories, etc under ACP > Community > Gallery > Add Category.
2) View "List Categories" page.
3) Then go back to add categories page, make mental note of the category orders in select menu/drop menu.
3) Go back to "List Categories" page again and reorder the top categories around a bit, changing their positions, and save it.
4) Go back to "add categories" page, and in select menu / drop menu for choosing a category to add a sub category too, or no parent etc. You'll notice the order of categories didn't change from the original ones created in step 1 and viewed for mental note in step 3.
The categories always seem to keep the original positioning when you first created initial top categories and sub categories in that select / drop menu listing the categories under "add category" page.