Hey @Honest Fox!
Make sure you're logged in with your Twitch account, then go to your default commands and make sure !commands is enabled.
By the way, you don't really need to set !commands' userlevel to Moderator, non-moderator chatters can't add/edit/delete a command even if !commands' userlevel is set to Everyone, when the !commands userlevel is set to Everyone, non-moderator chatters get as response from the bot a link to the commands list, hiding sensible information, it can be useful for your chatters to learn which commands they can use in your chat, only set the !commands userlevel to Moderator if you don't want your chatters to have access to your commands list (they still can get it by typing the correct URL in their browser tho').
Then, regarding the custom commands that don't work, if you add your commands through the chat and !commands was disabled, then the new custom commands weren't added, make sure that your new custom commands were actually added.
If you need further help, please provide the Twitch username with which you're having issues.