Hi all
If you are also receiving this error when unit testing your schemas:
TOMTreeGenerator.GetElementAbsoluteType: Object reference not set to an instance of an object.
then I can inform you that the reason is, that the built-in unit test framework does not support schemas that include or import other schemas.
To partially overcome this, take a look at the seventh issue of the BizTalk Hotrod at http://biztalkhotrod.com/default.aspx, where it is explained how to write a small helper class that will allow you to do unit testing on schemas that include and/or import other schemas.
Unfortunately this does not cover native file formats, but one can hope that Microsoft will improve the unit testing features in future versions of BizTalk.