After a great deal of frustration, I think I have finally narrowed down why some posts pingback with the full, pretty permalink, and some pingback with blogurl/?p=###. (I previously thought it had to do with something getting changed during upgrades.)
When I create a post and hit Publish immediately, it uses the full structure. If I save it as a draft first, or click on Advanced Editing, it uses the post ID instead.
Now I just need to figure out the new bug system...