The solution posted above means it's probably a conflict in the code of two features named identically.

Still a problem in July. This is ridiculous.

Edit: However I can confirm a relatively easy fix. Here's the process in more detail if anyone needs it:

1. Go to 'My Homebrew Creations' and create a new Subclass
2. Select the Paladin class and select whatever Subclass you're trying to fix as the template. In my case, I chose Oath of Redemption (XGtE)
3. Enter the Name as something like "Oath of Redemption (fixed)" or whatever you like. Enter a Short Description (I think you have to make this up) and a Description (copy and paste from the relevant subclass page)
4. You can leave all the other details as are (though you may or may not want to get rid of legacy versions of spells in the 'Additional Specific Spells' section). Click Save Changes.
5. Expand the Class Features section at the bottom and find the 'Channel Divinity' row. Click Edit in that row.
6. Change the name of this feature from 'Channel Divinity' to 'Channel Divinity (Redemption)' or something along those lines.
7. Scroll down and click Save Changes to update the feature.
8. You can now use your fixed version of the subclass on characters in your campaigns, and it should show the Channel Divinity checkboxes and extra options correctly