Andi, with regard to your request I will need some help as I don't know what 
you are asking me to do.
 
>Could you try the following: carry out those actions outside of 
>Fuseki/Joseki without inference.  It'll help pin down what's happening.
>
>You can use Fuseki as a standalong TDB installation (the server jar has 
>all the classes you need in it)
>
>>From the store at (1), load the new data either using arq.update (i.e. 
>applied the SPARQL Update.
>
>Issue a query.

My dataset in test.ttl originally looks as follows
 
urcscl003: tdbdump --loc=/tmp/TDB
<http://www.example.org/e1> <http://www.w3.org/2000/01/rdf-schema#label> 
"testunit" .
<http://www.example.org/e1> <http://purl.org/dc/elements/1.1#author> "mgi" .
<http://www.example.org/e1> <http://purl.org/dc/elements/1.1#date> "12/13/2011" 
.

After updating it with Fuskei as configured below - note that it does not 
matter whether I updated into service1 using #inf or service2 using #tdb - 
 
INSERT DATA {
<http://www.example.org/e2> <http://www.w3.org/2000/01/rdf-schema#label> 
"testunit" .
<http://www.example.org/e2> <http://purl.org/dc/elements/1.1#author> "mgi" .
<http://www.example.org/e2> <http://purl.org/dc/elements/1.1#date> "12/13/2011" 
.
}
 
the tdb store appears to contain
 
<http://www.example.org/e1> <http://www.w3.org/2000/01/rdf-schema#label> 
"testunit" .
<http://www.example.org/e1> <http://purl.org/dc/elements/1.1#author> "mgi" .
<http://www.example.org/e1> <http://purl.org/dc/elements/1.1#date> "12/13/2011" 
.
                                              
<http://www.w3.org/2000/01/rdf-schema#label> "testunit" .
                                              
<http://purl.org/dc/elements/1.1#author> "mgi" .
                                              
<http://purl.org/dc/elements/1.1#date> "12/13/2011" .

which crashes tdbdump but remarkably can be queried with service1 <#tdb> but 
not service2 <#inf>.
 
Attached is Fuseki version and configs. 
 
urcscl003: fuseki-server --version --config=tdbinfserv.ttl
Jena:       VERSION: 2.6.4
Jena:       BUILD_DATE: 2010-12-12T16:56:15+0000
ARQ:        VERSION: 2.8.9-SNAPSHOT
ARQ:        BUILD_DATE: 2011-09-14T21:54:22+0100
TDB:        VERSION: 0.8.11-SNAPSHOT
TDB:        BUILD_DATE: 2011-09-04T18:10:31+0100
Fuseki:     VERSION: 0.2.1-SNAPSHOT
Fuseki:     BUILD_DATE: 2011-09-15T08:18:13+0100

#####################
 
prefix fuseki:  <http://jena.apache.org/fuseki#> .
@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix ja:      <http://jena.hpl.hp.com/2005/11/Assembler#> .
@prefix tdb:     <http://jena.hpl.hp.com/2008/tdb#> .
[] rdf:type fuseki:Server ;
fuseki:services
( 
 <#service1>
 <#service2>
) .
<#service1> rdf:type fuseki:Service ;
 fuseki:name  "inf" ;
 fuseki:serviceQuery "sparql" ;
 fuseki:serviceQuery "query" ;
 fuseki:serviceUpdate "update" ;
 fuseki:serviceUpload "upload" ;
 fuseki:dataset  <#inf> ;
 .
<#service2> rdf:type fuseki:Service ;
 fuseki:name  "tdb" ;
 fuseki:serviceQuery "sparql" ;
 fuseki:serviceQuery "query" ;
 fuseki:serviceUpdate "update" ;
 fuseki:serviceUpload "upload" ;
 fuseki:dataset  <#tdb> ;
 .
[] ja:loadClass "com.hp.hpl.jena.tdb.TDB" .
tdb:DatasetTDB  rdfs:subClassOf  ja:RDFDataset .
tdb:GraphTDB    rdfs:subClassOf  ja:Model .
<#inf> rdf:type ja:RDFDataset ;
 ja:defaultGraph <#infmodel> ;
 .
<#infmodel> a ja:InfModel ;
 ja:baseModel <#tdbmodel> ;
 ja:reasoner [ja:reasonerURL 
<http://jena.hpl.hp.com/2003/RDFSExptRuleReasoner>] ;
 .
<#tdb> rdf:type ja:RDFDataset ;
      ja:defaultGraph <#tdbmodel> ;
 .
 
<#tdbmodel> rdf:type tdb:GraphTDB ;
      tdb:location "/tmp/TDB" ;
 .

##################################

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