I have this import element in my schema file:

<xsd:import namespace="Foo" schemaLocation="Foo.xsd" />

Everything works fine with Daffodil. Then, I add a letter to the beginning of Foo.xsd:

<xsd:import namespace="Foo" schemaLocation="AFoo.xsd" />

and, of course on my hard-drive I change the schema filename to AFoo.xsd

Using oXygen's validate capability I validated that I am importing the schema file correctly (so I know the import is correct).

Now when I run Daffodil it gives this error:

Schema Definition Error: Unable to import namespace Foo from XML catalog(s) jar:file ...

As far as I can tell the namespace and the file name must match.