Modified Content Types not reflected in Section Types Taxonomy

This is by design. The list of Section Types comes from the Taxonomy terms, not from the actual content types. When a content type is first created the taxonomy term is created with the same name. But after that you are able to change the name of the Taxonomy term to anything you want unrelated to the content type.

Sections are *not* supposed to be 1-to-1 mappings to content types. Sections Types are *layouts* of content. For example, a "Document Section" and a "News Section" both display content of type "oa-wiki-page" but have different layouts (document-focused files/folder layout vs News teaser listing)

Another example is the "Calendar Section". It's not displaying "calendar content type", it is displaying *Event* content type but using a Calendar *layout*. This is a really important architectural concept being Open Atrium.

Now, the "Node Types" checkboxes are also something else. Rather than directly tying these to content types, they actually represent "Command Buttons". If you look in Structure -> Command Buttons you'll see that a command button for creating a certain content type is created automatically when you initial create the custom content type. But again, once created they are then untied and you can edit the Caption of the command button to be anything you want.

This list of "Node Types" just controls the + dropdown menu for creating content within a Section. Using Command Buttons for that Create menu instead of direct content types allows you to add new custom menu items to the + menu. Command Buttons are just an indirect link mechanism that provides a Caption and Link that both accept tokens. This feature is used by some sites to allow very dynamic and extensible "Create +" menus within their sections.

So, the solution is to edit your Command Button captions (then clear cache) and then you'll see those reflected in the Node Types for your section type taxonomy.