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There could be several reasons why EF Core functions properly in a console app but not in a Windows Service. Some possible reasons are:

1. Permissions: Windows Service runs under a specific user account that may not have sufficient permissions to access the database. Ensure that the user account running the service has the necessary permissions.

2. Connection string: Make sure that the connection string used by the Windows Service is correct and points to the right database. Check for any typos or mistakes in the connection string.

3. Dependencies: Console apps and Windows Services may have different dependencies, and the Windows Service may be missing a required dependency to run EF Core properly. Ensure that all the necessary dependencies are present.

4. Environment: The environment in which the Windows Service runs may be different from that of the console app, affecting EF Core's behavior. Check for any environment differences and adjust accordingly.

5. Code: The code used in the console app may not be suitable for the Windows Service. Ensure that the code is written to be adaptable to different environments and situations.