I can reproduce the problem you're seeing. I'm not sure if the exact reason for it but I suspect it's related to the following message in the logs
WARN 2019-09-26 12:38:29,154 [stardog-user-4] com.clarkparsia.blackout.Saturator:saturate(104): Saturation was interrupted. Query results might be incomplete.
It looks like they might be incomplete and indeed it is. There's also the problem that there are a ton of axioms that are outside of the SL profile. I don't know what the expressivity of the ontology is but it's based on BFO so I suspect it may be OWL-Full or at least OWL-DL