Shawn,
This doesn't sound like a configuration issue with Portal Metrics as you are able to see API Reports. So I have a couple questions:
1. Is this happening with all applications? If you switch the specific application for the report, is it the same result?
2. Maybe this could be tied to a specific Org. If you switch the specific Org for the report, then chose another application under that new Org, is it the same result?
3. Can you ensure API's under that application are actually getting hit?
Thanks.
-Alec Daniello
APIM Support