Having two migration configurations in the same namespace is an unsupported scenario. We recently closed a bug like this one by design. The workaround is to have migration configurations in separate namespaces.
The most reliable solution to this problem is to simply place your configurations in different folders and use the MigrationsDirectory variable, as shown below, then any explicit migrations created for the configuration should be placed in the same folder
internal sealed class Configuration : DbMigrationsConfiguration<TestMultipleMigrationsScript.BlogContext>
{
public Configuration()
{
AutomaticMigrationsEnabled = false;
MigrationsDirectory = @"directory";
}
}
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