This is the console output running manually
nepomukservicestub nepomukstorage

Using Virtuoso Version: "6.1.3.3127-pthreads" 
Using Virtuoso Version: "6.1.3.3127-pthreads" 
void Soprano::VirtuosoController::writeConfigFile(const QString&, const BackendSettings&) "/tmp/virtuoso_C29840.ini" 
(LockFile) could not set lock for "/home/jtorres/.kde4/share/apps/nepomuk/repository/main/data/virtuosobackend/soprano-virtuoso.db" 
Shutting down Virtuoso instance (29768) which is in our way.
(LockFile) could not set lock for "/home/jtorres/.kde4/share/apps/nepomuk/repository/main/data/virtuosobackend/soprano-virtuoso.db"                                                           
(LockFile) could not set lock for "/home/jtorres/.kde4/share/apps/nepomuk/repository/main/data/virtuosobackend/soprano-virtuoso.db"                                                           
Starting Virtuoso server: "/usr/bin/virtuoso-t" ("+foreground", "+configfile", "/tmp/virtuoso_C29840.ini", "+wait") 
"
" 
"               Thu Nov 03 2011
" 
"20:25:03 OpenLink Virtuoso Universal Server
" 
"20:25:03 Version 06.01.3127-pthreads for Linux as of ??? ?? ????
" 
"20:25:03 uses parts of OpenSSL, PCRE, Html Tidy
" 
"20:25:03 Database version 3126
" 
"20:25:03 Entering Lite Mode
" 
"20:25:03 SQL Optimizer enabled (max 1000 layouts)
" 
"20:25:04 Compiler unit is timed at 0.000654 msec
" 
"20:25:06 Roll forward started
" 
"20:25:06 Roll forward complete
" 
"20:25:07 Checkpoint started
" 
"20:25:07 Checkpoint finished, log reused
" 
"20:25:07 Server online at 1113 (pid 29859)
" 
Virtuoso started: 29859 
Soprano::ODBC::ConnectionPool::ConnectionPool(const QString&, const QStringList&, QObject*) "host=localhost:1113;uid=dba;pwd=dba;driver=/usr/lib64/virtodbc_r.so" 
Soprano::ODBC::Connection::Connection() QThread(0x7f6b3a8341d0) 
"/opt/kde4/bin/nepomukservicestub(29840)" Soprano: "SQLGetData for data length failed (iODBC Error: [OpenLink][Virtuoso iODBC Driver]CL056: Bookmarks not enable for statement)"
bool Soprano::Virtuoso::DatabaseConfigurator::updateFulltextIndexRules(bool) empty rule name! 
virtual Soprano::ODBC::Connection::~Connection() QThread(0x7f6b3a8341d0) 
Soprano::ODBC::Connection::Connection() QThread(0x7f6b3a8341d0) 
Soprano::ODBC::Connection::Connection() Nepomuk::GraphMaintainer(0x7f6b2d4df120) 


And run under gdb, the stacktrace

#0  0x00007ffff433d014 in __strncmp_sse2 () from /lib64/libc.so.6
#1  0x00007fffe277099d in Soprano::ODBC::QueryResult::getData (this=0x7fffe14df380, colNum=1)
    at /g/kdegit/kdesupport/soprano/backends/virtuoso/odbcqueryresult.cpp:158
#2  0x00007fffe27680b7 in Soprano::Virtuoso::QueryResultIteratorBackend::binding (this=
    0x7fffe14df360, offset=0)
    at /g/kdegit/kdesupport/soprano/backends/virtuoso/virtuosoqueryresultiteratorbackend.cpp:197
#3  0x00007fffe2767d84 in Soprano::Virtuoso::QueryResultIteratorBackend::next (this=
    0x7fffe14df360)
    at /g/kdegit/kdesupport/soprano/backends/virtuoso/virtuosoqueryresultiteratorbackend.cpp:146
#4  0x00007fffe6eb8f88 in Soprano::Iterator<Soprano::BindingSet>::next (this=0x7fffffffb570)
    at /opt/kde4/include/Soprano/../soprano/iterator.h:239
#5  0x00007fffe6ebe01b in CrappyInferencer2::updateInferenceIndex (this=0x7fffe145d340)
    at /g/kdegit/kde-runtime/nepomuk/services/storage/crappyinferencer2.cpp:476
#6  0x00007fffe6ebe6c0 in CrappyInferencer2::CrappyInferencer2 (this=0x7fffe145d340, tree=
    0x7fffeebe6c10, parent=0x7fffe145d2c0)
    at /g/kdegit/kde-runtime/nepomuk/services/storage/crappyinferencer2.cpp:245
#7  0x00007fffe6eb11a6 in Nepomuk::Repository::open (this=0x7fffeebcfec0)
    at /g/kdegit/kde-runtime/nepomuk/services/storage/repository.cpp:213
#8  0x00007fffe6eb1ce4 in Nepomuk::Repository::qt_metacall (this=0x7fffeebcfec0, _c=
    QMetaObject::InvokeMetaMethod, _id=<optimized out>, _a=0x7fffee806f48)
    at /g/b45/kde-runtime/nepomuk/services/storage/repository.moc:85
#9  0x00007ffff7837ddc in QMetaObject::metacall (object=0x7fffeebcfec0, cl=
    QMetaObject::InvokeMetaMethod, idx=13, argv=0x7fffee806f48)
    at /g/kdegit/qt/src/corelib/kernel/qmetaobject.cpp:237
#10 0x00007ffff7847272 in QMetaCallEvent::placeMetaCall (this=0x7fffeeb86500, object=
    0x7fffeebcfec0) at /g/kdegit/qt/src/corelib/kernel/qobject.cpp:535
#11 0x00007ffff7848534 in QObject::event (this=0x7fffeebcfec0, e=0x7fffeeb86500)
    at /g/kdegit/qt/src/corelib/kernel/qobject.cpp:1217
#12 0x00007ffff52a4dfe in QApplicationPrivate::notify_helper (this=0x7fffee86b380, receiver=
    0x7fffeebcfec0, e=0x7fffeeb86500) at /g/kdegit/qt/src/gui/kernel/qapplication.cpp:4481
#13 0x00007ffff52a2444 in QApplication::notify (this=0x7fffffffcf10, receiver=0x7fffeebcfec0, 
    e=0x7fffeeb86500) at /g/kdegit/qt/src/gui/kernel/qapplication.cpp:3881
#14 0x00007ffff6851cce in KApplication::notify (this=0x7fffffffcf10, receiver=0x7fffeebcfec0, 
    event=0x7fffeeb86500) at /g/kdegit/kdelibs/kdeui/kernel/kapplication.cpp:311
#15 0x00007ffff782fd62 in QCoreApplication::notifyInternal (this=0x7fffffffcf10, receiver=
    0x7fffeebcfec0, event=0x7fffeeb86500)
    at /g/kdegit/qt/src/corelib/kernel/qcoreapplication.cpp:787


under valgrind there is no core dump, only warnings about uninitialized variables.