So far I have only verified that this is an issue when you have the following setup:

named root element -> sequence -> element with no name

In a test, if you specify the named root element as your root, it seems that the test is skipped. I tried debug mode but I still don't see any output for the test, and it isn't included in the test totals from the TDML runner. I first noticed this during multifile schema testing, because I was providing the element with a dfdl:ref and had gotten it confused with the ref property, thinking I didn't need to provide a name. I have since fixed the tests that was experiencing this issue, but if you need me to I can create another one and push it up for you to take a look.