I know this thread is old, but it's high on google...
I've had this problem, and it seems Hibernate is failing to deserialise an object, and so just returns a null. Setting a breakpoint on subclasses of HibernateException doesn't halt, so it's part of the internal logic somewhere.
The problem (in my case) is because the primary key mapping is invalid. I had a composite-key which had nulls for some of the columns (the database itself didn't have a primary key). Try changing(by removing columns) in the hbm.xml file until all the objects appear in the list of returned results.
In the example in this thread, some Objects are returned where Hibernate can create them (i.e. the key mapping for that Object is valid) whereas the nulls are inserted whenever the row can't be deserialised. To debug - add an order-by statement to the Hibernate query so the results are returned in a guarenteed order. Then match the rows in the database (by running the HQL query directly on the database) with the nulls to get an idea of why your Hibernate key is invalid.