Ruler annotations renamed as something starting with "M_" are saved and loaded correctly.

This is happening because the load data methods are trying to guess which type of annotation file you're trying to load. The internal hint is to rely on the default naming convention where rulers start with 'M'.

To override this assumption, click on the "Show Options" check box in the load data dialog and you can choose the annotation type from the radio buttons that appear.

Thanks. It works when the assumption is overridden.

Would it be possible to make the assumption based on the contents of the file since a fiducial annotation likely won't have ruler attributes?

Not easily as that would require reading all the files at the application level to check for formatting rather than relying on the extensions.