Table of Contents in alpha order InDesign

Try this: make sure all the boxes are checked for all your levels, then SAVE the style under a defined name. Each time you create the TOC or update it, make sure that style is selected.

One of the many quirks of the TOC feature is that it loses settings in between executions. You can set a number of things and create a TOC, but when you try to repeat that, the 'style' will have reset to the default. That may be what's happening to you, in part.

If not, you may need to reset your InDesign preferences. When they get corrupted, all kinds of screwy things happen, especially with the indexing, note, TOC etc. features. Search this forum; there are several threads that give details of how to reset prefs for each platform and version.