Nikos said:
Apart of missing shortcuts and missing settings of some applications which i reconfigured i run Repair Windows ALL in one just in case and all seems to work as expected for the time being.
That is only a temporary fix Nikos. It is strongly advised at this point to create a backup of your programs (installers that is), pictures, documents, bookmarks and other personal stuff into an external hard disk or dvd's and then re-install windows 7 from scratch.
Once that is done, update Windows 7 and the drivers. Then create a backup.
Next step would be starting to install the applications, restart and then backup once again.
At this stage you have two backups, one fully updated with Windows 7 Clean, the other one with the same but with your applications installed.