In the test set file All.testSet from Saxonica the following XSD 1.1 test seems to be wrongly specified:

<testGroup name="all004"
  -> <instanceTest name="all004.v02.xml">

The expected validity of this test is specified as "valid". I believe when instance document all004.v02.xml is attempted to be validated with schema all004.xsd a compliant XSD 1.1 processor must return an "invalid" outcome (the reasons for this are specified below).

In the schema document mentioned above, the element declaration specifies:
<xs:element name="doc" nillable="1">
  ..
</xs:element>

and the instance document is as follows:
<doc xsi:nil="1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">


</doc>

Since there are whitespace child nodes within element "doc", the contents of element "doc" are not strictly empty.

To rectify this test case, I would suggest either of following measures:
1. Modify the instance document to remove whitespace children within element "doc", i.e corrected instance document would then be,
<doc xsi:nil="1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" />

OR

2. Modify the test spec of test <instanceTest name="all004.v02.xml">
to say expected validity as "invalid".