Error while accessing Entity Framework 6 context

Question

I have problem related to Entity Framework 6, migrations and context.

I have created DbMigration like this:

    public override void Up()
    {
        CreateTable(
            "dbo.Settings",
            c => new
            {
                Id = c.Int(nullable: false, identity: true),
                Name = c.String(),
                Value = c.String(),
            })
            .PrimaryKey(t => t.Id);

        Sql("SET IDENTITY_INSERT[dbo].[Settings] ON");

        Sql("INSERT[dbo].[Settings]([Id], [Name], [Value]) VALUES(1, N'Name1', N'Value1')");
        Sql("INSERT[dbo].[Settings]([Id], [Name], [Value]) VALUES(2, N'Name2', N'Value2')");

        Sql("SET IDENTITY_INSERT[dbo].[Settings] OFF");
     }

In configuration I have

    public Configuration()
    {
        AutomaticMigrationsEnabled = true;
    }

    protected override void Seed(MyContext context)
    {
    }

and DbContext

    public MyContext() :
        base(connectionString)
    {
        Database.SetInitializer(new MigrateDatabaseToLatestVersion<MyContext, Migrations.Configuration>());
    }

Every time when I perform any operation on context, such as:

var ctx = container.Resolve<IMyContext>() as MyContext;
ctx?.Database.Initialize(false);

or I access it by a DbSet:

DbSet<Settings> Set => this._Context.Set<Settings>();
var setting = this.Set.FirstOrDefault();

I get an exception:

System.Data.SqlClient.SqlException: 'There is already an object named 'Settings' in the database.'

After changing configuration to

AutomaticMigrationsEnabled = true;

the exception becomes:

System.Data.Entity.Migrations.Infrastructure.AutomaticMigrationsDisabledException: 'Unable to update database to match the current model because there are pending changes and automatic migration is disabled. Either write the pending model changes to a code-based migration or enable automatic migration. Set DbMigrationsConfiguration.AutomaticMigrationsEnabled to true to enable automatic migration.'

I have tried other advice with adding empty migration: Initial, without any success.

Somehow, accessing context tries to re-create this table (and others). Did I miss something in the settings ? After several hours I'm stuck.

Thank you