> And you are running HDT jars as hdt-java provide? (which are for Apache Jena 3.0.1 IIRC)
mmm yes it could be. What I do is - download https://github.com/rdfhdt/hdt-java - build - edit the Fuseki startup script as described here http://www.rdfhdt.org/manual-of-hdt-integration-with-jena/ - start Fuseki It works nicely though, so far only this query has given this kind of problems.