To test this, create a module in a Coldbox app with these CFCs:
/modules_app/myModule/models/foo/test.cfc (alias as fooTest@myModule)
/modules_app/myModule/models/bar/test.cfc (alias as barTest@myModule)
/modules_app/myModule/models/baz/test.cfc (alias as bazTest@myModule)
WireBox will only pick up the first mapping because the mappings keep overwriting each other before they are processed. Change how mapDirectory() works in the binder to force the mappings and process them immediately.