I spent a few hours on this issue and if I hadn’t had a colleague help me fix the issue I’d probably still be working on it.
The issue was I’d created 2 custom list instance in Visual Studio and deployed them. The first list inherited the content type assigned to it but the second one wouldn’t, it would take the first lists content type. The fix for the issue ,which in no way is obvious it the list template type id.
Description=”My List Definition”
In the template you have the type which is normally between 100 and 200, this is where the issue lies. SharePoint has apparently reserved these numbers between 100 and 10,000 for it self. All I needed to do was ad a number over 10,000 and it worked fine.