These properties are controlled per-relationship basis. If you are on Database-First, they are pulled from your FK metadata at your DB. If you are on Model-First, they are controlled by Project Settings / Designer Preferences.
You also can right-click a relationship and click 'Edit' then you can change those. So, IMHO, some process (change in your DB, change in your model, a plugin, or something else) must be changing them. More info on the documentation.
Also, make sure you don't mention the exact LLBLGen Designer will that you are using. Make sure that you are using the latest, as a fix was made about this some time ago on v4.0: http://www.llblgen.com/TinyForum/Messages.aspx?ThreadID=22049&StartAtMessage=0𞗠