Category management glitch

I’ve got a site with a fairly complex set of categories with sub-cats, sometimes 5 layers deep in places. On the public side, we’re using WP-dTree to draw them out as a collapsible list, and they all show up nicely.

HOWEVER, in the admin area, I’m finding whole branches of the tree are disappearing. Some sections just don’t show up, but their sibling sections draw perfectly. And when I choose page 2 to view more categories, the second page is empty (draws the header and footer of the table, but no content inside).

What I’ve tried:
– I changed the admin PHP pages to draw 1,000 categories on each page, on the off change that it would help (maybe it was having trouble deciding how to draw children within the paging limit?). Doesn’t do anything except remove the “page 2” option.
– I found the ID for one of the missing cats and edited it directly, but even after changing the slug and the name, nothing appeared. Can’t delete cats from the edit page, either, which is a bit of a UI oddity, I’m finding.
– I went into the database and removed the entire branch manually, then put it back in. It worked up to a point, and then stopped showing a different branch of the tree seemingly at random.
– Made sure there were no strange names or characters in the slug names that might be making WP choke. They’re all fine.

At this point, I think my only hope is to find a different category manager, because when I hand this site off to the client, I can’t have this happening to them. Does anyone know any good plugin alternatives, or if not… any idea why this would be happening?

Thanks in advance!