Differences in the way empty directories are fetched using JBE vs API

We've found an issue in the way empty directories are handled during fetching.

Some of our RTC builds use the Jazz Build Engine to fetch files and this does not fetch empty directories in the source stream. However, some of our builds are run on TeamCity using a plugin that was written. This plugin is using java code which is what the RTC ant task "teamFetch"  uses:

            final LoadOperation loadOp = (LoadOperation) IOperationFactory.instance
            .getLoadOperation(handler);

This does fetch empty directories.

I'd like to understand the options in making this consistent:
1. Is there a way to make the JBE fetch empty directories?
2. Is there a way in java code to not fetch empty directories?

Thanks.