I personally made a first update on my update-test-disk and it was completely OK. Reassured, I did it on my main disk and then I started having some really annoying problems, especially systems freeze of 1 or 2 second after each click of an icon or a menu. So I Tried some classic repair tools with no success.
Then I took the time to reinstall completely, well, 1... 2... 3, maybe 4 times completely before understanding what triggered this problem : it seems to be linked with the offline update image (.dmg from Apple site). On my test disk, I had used Software Update !
So what I did was downloading the 10.9.1 installer from the Mac App Store and building my install USB drive with Unibeast. Install of the 10.9.1 version worked like a charm and now I'm back with a perfectly working hackintosh. In my case, everything seems to point the offline updater as the culprit : I hope this will help.
Thanks to all.