Can you reproduce under a new user? Also, can you confirm your system is fully upgraded?

Sorry for the late answer.

I haven't tried creating a new user , but I tried wiping out the entire .kde4 directory.

Right now I'm updating to the new 4.4.1, if the issue persist I'll try your suggestion and ... in case your suggestion works , what is supposed I should do?

Running the command referred to by admin in his post caused my KDE basket to revert to a default KDE basket. Since I keep my life in there, I was very disturbed. However, if this happens to you the fix is actually quite easy:

Make sure basket isn't running, choose quit from menu, don't leave it running in the tray.

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mv "$(kde4-config --localprefix)/share/apps/basket" ~/my-real-basket
mkdir "$(kde4-config --localprefix)/share/apps/basket"

Start basket up again, you are looking at am empty basket which has only "General" in it. Close it from the File menu using quit, again make sure it's not just in your system tray.

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rm -rf "$(kde4-config --localprefix)/share/apps/basket"
mv ~/my-real-basket "$(kde4-config --localprefix)/share/apps/basket"

Run basket again and it magically rebuilds it's index.

And thank you for all the advice including admin who scared me greatly since this thread fixed my desktop search too

KDE 4.5

When I start nepomukserver I get the following message:
[/usr/bin/nepomukservicestub] Using Virtuoso Version: "6.1.2.3127-pthreads"
Using Virtuoso Version: "6.1.2.3127-pthreads"
void Soprano::VirtuosoController::writeConfigFile(const QString&, const Soprano::BackendSettings&) "/tmp/virtuoso_XM8229.ini"
Starting Virtuoso server: "/usr/bin/virtuoso-t" ("+foreground", "+configfile", "/tmp/virtuoso_XM8229.ini", "+wait")
[/usr/bin/nepomukservicestub] "
"
[/usr/bin/nepomukservicestub] " Tue Nov 30 2010
"
[/usr/bin/nepomukservicestub] "19:45:58 OpenLink Virtuoso Universal Server
"
[/usr/bin/nepomukservicestub] "19:45:58 Version 06.01.3127-pthreads for Linux as of Nov 22 2010
"
[/usr/bin/nepomukservicestub] "19:45:58 uses parts of OpenSSL, PCRE, Html Tidy
"
[/usr/bin/nepomukservicestub] "19:45:58 Database version 3126
"
[/usr/bin/nepomukservicestub] "19:45:58 Entering Lite Mode
"
[/usr/bin/nepomukservicestub] "19:45:58 SQL Optimizer enabled (max 1000 layouts)
"
[/usr/bin/nepomukservicestub] "19:45:58 GPF: disk.c:822 buf fill anomaly
"
[/usr/bin/nepomukservicestub] "GPF: disk.c:822 buf fill anomaly
"
[/usr/bin/nepomukservicestub] Virtuoso server stopped: 2
[/usr/bin/nepomukservicestub] "/usr/bin/nepomukservicestub(8229)" Soprano: "Failed to start Virtuoso"
[/usr/bin/nepomukservicestub] "/usr/bin/nepomukservicestub(8229)" Soprano: "Failed to start Virtuoso"
Application '/usr/bin/nepomukservicestub nepomukstorage' exited normally...

Akonadi Agent gives the following message about Nepomuk:

Calling the Nepomuk storage service failed: 'The name org.kde.NepomukStorage was not provided by any .service files'.

Is there another version of Virtuoso I should be using?

Looks like your Virtuoso database is corrupt. Please run the following outside KDE:

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rm -rf $(kde4-config --localprefix)/share/apps/nepomuk/

I did ctrl-alt-F3 and ran
rm -rf $(kde4-config --localprefix)/share/apps/nepomuk/
I verified that there was no nepomuk directory in ~/.kde4/share/apps/
I did ctrl-alt-F7 to get back KDE
I verified that akonadi was not running by running akonodictl stop
I ran qdbus org.kde.NepomukServer /nepomukserver quit
I ran nepomukserver &
I received the same error message about "Failed to start Virtuoso"
Here is my current nepomukserverrc
[Basic Settings]
Configured repositories=main
Start Nepomuk=true

[Service-nepomukstrigiservice]
autostart=true

[main Settings]
Maximum memory=41
Storage Dir[$e]=$HOME/.kde4/share/apps/nepomuk/repository/main/
Used Soprano Backend=Virtuoso
rebuilt index for type indexing=true

Is there a problem with my systemsettings?

New info:
I logged out of my user and logged in as root for the first time since upgrading to KDE4.5. Nepomuk automatically converted itself from redland to Virtuosobackend, and there do not appear to be any problems. When I check ~/.kde4/share/apps/nepomuk/repository/main/data/ there is no redland directory, and the virtuosobackend is missing the file soprano-virtuoso.trx
How can I correct this?
Should I delete ~/.kde4/share/apps/nepomuk/ using kde4config again?

You need to have Nepomuk stopped when running the command I gave for it to work correctly. Also, ensure all "virtuoso-t" processes are not running.

I verified that akonadi was stopped, nepomuk and virtuoso-t were not running, and then renamed nepomuk*rc in ~/.kde4/share/config because of another entry I saw in this forum. I logged out of KDE4 and logged into the console. I removed the ~/.kde4/share/apps/nepomuk directory again, and logged back into KDE4.

It looks like it's working! Thanks for your help and patience with this.