app.config

<?xml version="1.0" encoding="utf-8" ?>
<configuration>
    <startup> 
        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.5.1" />
    </startup>
  <system.data>
    <DbProviderFactories>
      <add name="SQLite Data Provider" invariant="System.Data.SQLite"
         description="ADO.NET Data Provider for SQLite"
         type="System.Data.SQLite.SQLiteFactory, System.Data.SQLite, Version=1.0.94.0, Culture=neutral, PublicKeyToken=db937bc2d44ff139" />
    </DbProviderFactories>
  </system.data>
</configuration>

main.cs

    class Program
    {
        static void Main(string[] args)
        {
            var stores = new List<string>
            {
                "user_eventstore",
                "registration_eventstore",
                "project_eventstore",
                "authentication_eventstore",
            }
            .Select(CreateStore)
            .ToList();

            using (var stream = stores[0].CreateStream(Guid.NewGuid()))
            {
                stream.Add(new EventMessage
                {
                    Body = new object()
                });

                stream.Add(new EventMessage
                {
                    Body = new object()
                });

                stream.CommitChanges(Guid.NewGuid());
            }

            var storeCounts = stores.Select(x => x.Advanced.GetFrom(null))
                                            .SelectMany(x => x)
                                            .SelectMany(x => x.Events)
                                            .ToList();

            var total = storeCounts.Count(); // 40 instead of 10
            Console.WriteLine(total);
            Console.ReadLine();
        }

        private static IStoreEvents CreateStore(string name)
        {
            var file = Path.Combine(Environment.CurrentDirectory, name + ".db");
            var connectionString = string.Format("Data Source={0};Version=3;UseUTF16Encoding=True;",file);
            if(!File.Exists(file)) SQLiteConnection.CreateFile(file);
            return Wireup
                .Init()
                .UsingSqlPersistence(name, "System.Data.SQLite", connectionString)
                .WithDialect(new SqliteDialect())
                .InitializeStorageEngine()
                .Build();
        }
    }

packages.config

<?xml version="1.0" encoding="utf-8"?>
<packages>
  <package id="NEventStore" version="5.1.0" targetFramework="net451" />
  <package id="System.Data.SQLite.Core" version="1.0.94.0" targetFramework="net451" />
</packages>