WARNING: You have Products in the Top Level Category

I've searched, but haven't run across a solution for this specifc issue.

We have recently upgraded to Zen 1.3.8a and added all patches. We notced we cannot add Categories to theTop level categories now. We see teh error:

WARNING: You have Products in the Top Level Category. This will cause pricing to not work properly in the Catalog. Products found: 1

Here's where it's different then any of the other posts. On the same page it shows us ther are:

Categories: 16
Products: 0

Visually we only see Categories in the top level. We are not seeing any products. What could have caused this?

Just a guess, but it's possible that the admin display code only displays categories or products, not both in the same listing.
I know that the catalog side will only display the product listing if a category has products and subcategories.

You may need to go into the database and (very carefully) find and delete or move the offending product. Others can give details of how to do this.

Look for products with master categories 0 in database. This happen to me a lot when I upload products using EP. But I do see the product in the top level category and can delete it which make the warning disappear. Usually these products will show as master category 0.