EF6 Code First Migration Seed Method not able to create users

Question

I have implemented Identity 2.1 with custom classes to make all of the entities to have integer keys.

I have the following seed method in my configuration.cs file in the migrations folder

protected override void Seed(ApplicationDbContext context)
{
    var roleManager = new ApplicationRoleManager(new ApplicationRoleStore(context));
    var userManager = new ApplicationUserManager(new ApplicationUserStore(context));

    if (!roleManager.RoleExists("User"))
    {
        roleManager.Create(new ApplicationRole("User"));
    }
    if (!roleManager.RoleExists("Supervisor"))
    {
        roleManager.Create(new ApplicationRole("Supervisor"));
    }
    if (!roleManager.RoleExists("Administrator"))
    {
        roleManager.Create(new ApplicationRole("Administrator"));
    }
    if (!roleManager.RoleExists("Owner"))
    {
        roleManager.Create(new ApplicationRole("Owner"));
    }
    if (!roleManager.RoleExists("System User"))
    {
        roleManager.Create(new ApplicationRole("System User"));
    }

    if (userManager.FindByName("h2euser") == null)
    {
        var h2Euser = new ApplicationUser
        {
            UserName = "h2euser",
            Email = "test"
        };
        var result = userManager.Create(h2Euser, "Letme1n");

        if (result.Succeeded)
        {
            userManager.AddToRole(h2Euser.Id, "System User");
        }
    }

    if (userManager.FindByName("owner") == null)
    {
        var ownerUser = new ApplicationUser
        {
            UserName = "owner",
            Email = "test2"
        };

        var result = userManager.Create(ownerUser, "ChangeMe!");

        if (result.Succeeded)
        {
            userManager.AddToRole(ownerUser.Id, "Owner");
        }
    }
}

When running the Update-Database method I get this error:

System.Data.Entity.Core.EntityCommandExecutionException: An error occurred while executing the command definition. See the inner exception for details. ---> MySql.Data.MySqlClient.MySqlException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'FROM ((SELECT CASE WHEN (`Extent2`.`UserId` IS NULL) THEN (NULL) ELSE (1) END' at line 33

My UserStore:

public class ApplicationUserStore
 : UserStore<ApplicationUser, ApplicationRole, int,
     ApplicationUserLogin, ApplicationUserRole,
     ApplicationUserClaim>
{
    public ApplicationUserStore()
        : this(new IdentityDbContext())
    {
        base.DisposeContext = true;
    }


    public ApplicationUserStore(DbContext context)
        : base(context)
    {
    }
}

And my user manager:

 public class ApplicationUserManager : UserManager<ApplicationUser, int>
{
    // *** ADD INT TYPE ARGUMENT TO CONSTRUCTOR CALL:
    public ApplicationUserManager(IUserStore<ApplicationUser, int> store)
        : base(store)
    {
    }

    public static ApplicationUserManager Create(IdentityFactoryOptions<ApplicationUserManager> options, IOwinContext context)
    {
        // *** PASS CUSTOM APPLICATION USER STORE AS CONSTRUCTOR ARGUMENT:
        var manager = new ApplicationUserManager(
        new ApplicationUserStore(context.Get<ApplicationDbContext>()));

        // Configure validation logic for usernames

        // *** ADD INT TYPE ARGUMENT TO METHOD CALL:
        manager.UserValidator = new UserValidator<ApplicationUser, int>(manager)
        {
            AllowOnlyAlphanumericUserNames = false,
            RequireUniqueEmail = true
        };

        // Configure validation logic for passwords
        manager.PasswordValidator = new PasswordValidator
        {
            RequiredLength = 6,
            RequireNonLetterOrDigit = true,
            RequireDigit = true,
            RequireLowercase = true,
            RequireUppercase = true,
        };

        // Configure user lockout defaults
        manager.UserLockoutEnabledByDefault = true;
        manager.DefaultAccountLockoutTimeSpan = TimeSpan.FromMinutes(5);
        manager.MaxFailedAccessAttemptsBeforeLockout = 5;

        // Register two factor authentication providers. 

        // This application uses Phone and Emails as a step of receiving a 
        // code for verifying the user You can write your own provider and plug in here.

        // *** ADD INT TYPE ARGUMENT TO METHOD CALL:
        manager.RegisterTwoFactorProvider("PhoneCode",
            new PhoneNumberTokenProvider<ApplicationUser, int>
            {
                MessageFormat = "Your security code is: {0}"
            });

        // *** ADD INT TYPE ARGUMENT TO METHOD CALL:
        manager.RegisterTwoFactorProvider("EmailCode",
            new EmailTokenProvider<ApplicationUser, int>
            {
                Subject = "SecurityCode",
                BodyFormat = "Your security code is {0}"
            });

        var dataProtectionProvider = options.DataProtectionProvider;

        if (dataProtectionProvider != null)
        {
            // *** ADD INT TYPE ARGUMENT TO METHOD CALL:
            manager.UserTokenProvider =
                new DataProtectorTokenProvider<ApplicationUser, int>(
                    dataProtectionProvider.Create("ASP.NET Identity"));
        }
        return manager;
    }
}