Protege 5.0.0 Build beta-15 (though I think I get the same from Protege 4.3 files) File saved as turtle. Reproducible.
From terminal:
My-MacBook-Air:bin twostewards_fb$ ./stardog-admin db create -n test ~/test.owl
Bulk loading data to new database.
Parsing triples: 100% complete in 00:00:00 (0 triples - 0.0K triples/sec)
Parsing triples finished in 00:00:00.048
Creating index: 100% complete in 00:00:00 (0.0K triples/sec)
Creating index finished in 00:00:00.006
Loading complete.
Inserted 0 triples in 00:00:00.569 at 0.0 triples/sec
Bulk load complete. Loaded 0 triples from 1 file(s) in 00:00:00 @ 0K triples/sec.
Errors were encountered during loading:
File: /Users/twostewards_fb/Downloads/test.owl Message: Content is not allowed in prolog. [line 1, column 1]
Successfully created database 'test'.
My-MacBook-Air:bin twostewards_fb$ cat ~/test.owl
@prefix : <http://www.semanticweb.org/twostewards_fb/ontologies/2014/5/untitled-ontology-77#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@base <http://www.semanticweb.org/twostewards_fb/ontologies/2014/5/untitled-ontology-77> .
<http://www.semanticweb.org/twostewards_fb/ontologies/2014/5/untitled-ontology-77> rdf:type owl:Ontology .
#################################################################
#
# Classes
#
#################################################################
### #test
<#test> rdf:type owl:Class .
### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net
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