Entity Framework 6 migrations odd behaviour

Question

I am using EF6 Code First with migrations in a new project. I have used this in a few projects already without issue.

Now this new project is against an existing database. I generated the standard Initial migration file, then deleted all the contents leaving just the Up() and Down() methods. This has worked for me in other projects, but not this time.

When I run update-database from the Package Manager Console, all works as expected.

PM> update-database
Specify the '-Verbose' flag to view the SQL statements being applied to the target database.
No pending explicit migrations.
Running Seed method.

Then I execute the migrations from code (as needed in production) and I get...

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 been trying to get my head around this one for two days, and not getting anywhere. I have even added another migration file called "stub" and it is generated blank. EF does not see any changes to my model (of which there are none), so it has nothing to generate. Yet the migration execution via code persists with the error that there are migrations pending.

I have attached a logger to the code execution of the migrations and the output is this.

Target database is: 'FMS' (DataSource: (local)\SQL2012, Provider: System.Data.SqlClient, Origin: Configuration).
No pending explicit migrations.

And then I get the error message in my browser.

My configuration class

namespace FMS.Infrastructure.Repository.EF.Migrations.Stage
{
    public sealed class StageConfiguration : DbMigrationsConfiguration<StageDb>
    {
        public StageConfiguration()
        {
            AutomaticMigrationsEnabled = false;            
            MigrationsDirectory = @"Migrations\Stage";
            CommandTimeout = 3000;
            ContextKey = "FMS.Stage";
        }        
    }
}

And the code that performs the migrations

Database.SetInitializer(new MigrateDatabaseToLatestVersion<StageDb, StageConfiguration>());

var dbMigrator = new DbMigrator(new StageConfiguration());

var logger = new MigratorLoggingDecorator(dbMigrator, new DbMigrationLogger());

foreach (string migration in dbMigrator.GetPendingMigrations())
    Console.WriteLine(migration);

logger.Update();

I hope this is clear enough for those willing to try assist. If anyone has a tip, I am all ears. This is making me grey.