Doc Library webpart "New" button missing

So, we isolated the code where this goes wrong.

"updatedList" here is our document library where we add custom content types through code

var updatedListCTs = updatedList.ContentTypes;
Context.Load(updatedListCTs);
Context.ExecuteQueryRetry();

//loading the CTs from the web where we have our Doc Lib

ContentTypeCollection siteCTs = Context.Web.ContentTypes;
Context.Load(siteCTs);
Context.ExecuteQueryRetry();

//here we add one of the web CT to the Doc Lib

updatedList.ContentTypes.AddExistingContentType(siteCT);

updatedList.Update();
Context.ExecuteQueryRetry();

At this point, the New button is gone for all users except the SP Admin user.