Category Order

I don’t understand what’s happening on my site. v2.9.3 - Build Date: 20150427

I have nested categories within a category group, they are set to Custom Sort Order, but I can only change the order of some categories. Others appear stuck, I can click the up/down buttons all I want and the page refreshes with no change. I see bugs about this in version 2.1.3 but I would think they’re fixed now. Any idea what’s going on? Is there some reliable way to set the sort order of categories without using the up/down arrows in Admin > Channel Admin > Categories?