Anyone else have this problem? I am attempting to reorganize my icons in the menu, and after doing so, and pushing done, they immediately go back to alphabetical.

Anyone know what file I need to alter to prevent this from happening?

2d

Well, you're not the only with that problem. but here, it has some "random" icons at first. Then, if you scroll down, it's alphabetically ordered. I can't change icons that are in the end (Web, Phone, E-mail, etc) to the Top lines. But i can change those between them (let's say, changing to the left).
The first icons, (until "Shop" appears) can't be moved.

I would really appreciate an answer on how to fix or if it will be fixed.

Well, i installed mymenu and now it's well categorized exactly how i like it
You can install it through Extras-Testing or Extras-Devel, i can't remember.
it's an alternative for that problem