Wiki Pages aren't in Alphabetical Order...

Thanks Rachel Jackson , that makes a lot more sense.

I have a few thoughts:

1. When creating a Wiki page, it defaults to the bottom of the list in the Options that Tom mentioned and you say isn't loading for you. Since you say it's only happening to the new pages, my assumption is the list isn't loading, but it still functions like it is on saving the new page:
   
2. The Options not showing is probably a bigger issue. I don't know if there's a limit you've hit, but I would do some basic troubleshooting to rule that out (Try it in another browser, try as another user, try in Incognito/Private browsing, try in another group on your community) and then probably open a Support case to have them check your community to narrow down the cause. There might be some server-side errors you're not aware of, for instance. 
3. There is not a Sort option on the TOC and being able to manipulate the order of the TOC and page nesting is an important feature for many situations. I see the benefit from your standpoint though, but none of the wikis on my community are alphabetized and are instead grouped by like-pages, or importance, or some other method. I'd suggest creating an Product Ideas and Improvements  to request sorting options on the TOC in Wikis (alphabetical, date created, date modified, etc). 
4. Maybe a different widget instead of the TOC widget could help. For example, if you do some changes in Widget Studio, maybe you can make the Wikis - Page List widget work for you properly. We have the  widget from Social Edge (Sara Collins can probably tell you more) and seems like that would work perfectly for you too. 

I hope this helps!