Entity Framework not generating INNER JOIN with .Include - entity-framework

Question

I have a project where an .Include does not generate an INNER JOIN, while the INNER JOIN is generated in other projects using the same DbContext and code.
I am using EF Core Code-First. The DbContext is shared with other projects through NuGet.
Below are the two classes in question and their configuration in the DbContext:
[Table("Project", Schema = "ProjectManagement")]
public class AxosoftProject
{
[Key, DatabaseGenerated(DatabaseGeneratedOption.None)]
public int AxosoftId { get; set; }
public int? AxosoftParentId { get; set; }
public AxosoftProject AxosoftParent { get; set; }
public List<AxosoftProject> Children { get; set; }
public string Name { get; set; }
public bool IsActive { get; set; }
public string Description { get; set; }
public DateTime? StartDate { get; set; }
public DateTime? EndDate { get; set; }
public DateTime UpdateDate { get; set; }
public ICollection<AxosoftItem> Items { get; set; }
}
[Table("Item", Schema = "ProjectManagement")]
public class AxosoftItem
{
[Key, DatabaseGenerated(DatabaseGeneratedOption.None)]
public int AxosoftId { get; set; }
public int AxosoftProjectId { get; set; }
public AxosoftProject AxosoftProject { get; set; }
public string Name { get; set; }
public string ItemType { get; set; }
public string SubItemType { get; set; }
public decimal PercentComplete { get; set; }
public DateTime UpdateDate { get; set; }
}
DbContext:
modelBuilder.Entity<AxosoftProject>().HasKey(x => x.AxosoftId);
modelBuilder.Entity<AxosoftProject>().HasOne(x => x.AxosoftParent).WithMany(x => x.Children);
modelBuilder.Entity<AxosoftProject>().HasMany(x => x.Items);
modelBuilder.Entity<AxosoftItem>().HasKey(x => x.AxosoftId);
modelBuilder.Entity<AxosoftItem>().HasOne(x => x.AxosoftProject);
Code to query all projects and their items:
IMyEntities MyEntities = new MyEntities("Server=localhost;Database=MyEntities;Trusted_Connection=True;MultipleActiveResultSets=true");
var projects = MyEntities.AxosoftProjects.Include(x => x.Items).ToList();
var listwithitems = projects.Where(x => x.Items != null).ToList();
Depending on the project that I execute above code in, it will either do an INNER JOIN or no INNER JOIN at all. I tried deleting the whole project where above code does not perform an INNER JOIN, cloning it from the repository afterwards to start from fresh, still no INNER JOIN.
How do I go about debugging this further? I suspect the project where it doesn't work may be using an old version of the DLL's even if it looks like it's pointing to the correct ones.
UPDATE
To verify that the include is indeed not working, I did an additional test. If I load the AxosoftItems into the DbContext seperately, then EF will populate the Items collections for each AxosoftProject. Example:
var projects = MyEntities.AxosoftProjects.Include(x => x.Items).ToList();
var listwithitems1 = projects.Where(x => x.Items != null).ToList(); // 0 items
var items = MyEntities.AxosoftItems.ToList();
var listwithitems2 = projects.Where(x => x.Items != null).ToList(); // 41 items
UPDATE 2
The code and reference to EF Core was placed in an ASP.NET MVC project. Moving the code to a separate class library "fixes" the issue, the INNER JOIN is not ignored, and the code is exactly the same. I intend to download the source code and debug my way through, to figure out why the Include is being ignored in the MVC project.