Hi Shawn,
Welcome to the Method forum! My apologies for the late reply.
The customer reports actually use the Contacts table as the master table. As such, the dropdown for custom reports is filtered for reports with Contacts as the master table.
You have a couple of options with how to go about this.
1. Use the Contacts table as the master table for your report.
or
2. Filter the custom report dropdown for reports with the Contacts table or the Customer table as the master table. You can accomplish this by using the Build Selection List instead of Equal to value in the Filter dropdown.
--Audisho