I started with one of the built-in multilevel lists. After I set up the format of the text following the numbers/letters of the list (I wanted them in CTRL+Shift+A all caps so the sections would appear as regular text in my TOC), I highlighted each list level and added it as a new style. Then, I changed the format of a couple of the list levels (for example, I changed the built-in default "a)" to "i.").

Sometime after, I noticed the misalignment. Tried everything I know to fix it, but no dice.

To explain my actions above, the document I'm trying to create is a journal article that liberally uses multi-level headings. I want those to appear in an update-able table of contents (hence the use of styles).

Does that help? Happy to provide any other information.