Some directories could not be loaded, trying to sync items through Unicorn.

[MortenSkjoldager]

Do you want to request a feature or report a bug?
Bug
What is the current behavior?
Programatically syncing configuration breaks, but doing this through Unicorn.aspx works fine.

If the current behavior is a bug, please provide the steps to reproduce.

Trying to import configuration and Yaml files programmatically with the following code snippet:

public virtual void SynchroniseTargetDataStore(IConfiguration configuration)
		{
			var logger = configuration.Resolve<ILogger>();
			var helper = configuration.Resolve<SerializationHelper>();

			try
			{
				logger.Info(string.Empty);
				logger.Info("Unicorn.Bootstrap is syncing " + configuration.Name);

				var pathResolver = configuration.Resolve<PredicateRootPathResolver>();

				using (new EnforceVersionPresenceDisabler())
				{
					helper.SyncTree(configuration);
				}
			}
			catch (Exception ex)
			{
				logger.Error(ex);
				throw;
			}
		}

I have also tried to sync each subtree, same result.
what is the difference between synctree and syncconfiguration? I tried to .peek the sync verb and that seems to run syncconfiguration. That seems like it is not an option for me in this case?

What is the expected behavior?
Sync should work without an exception "some directories could not be loaded".
Please mention your Sitecore version and Unicorn version.

Sitecore 9.2, Unicorn 4.1.1