2009 Mac Pro boots but will not go to desktop only RAID card utility.

After restarting the RAID card utility appears and asks to open or cancel. This is normal, it has always done this. If you cancel, only background image is on screen, nothing else but the mouse. If I open the utility the RAID info shows with the HD's. I also see menu item at the top including the apple. I can open system Prefs, recent items but no desktop. Mac boots in safe mode and shows all desktop items, apps and HD's. I boot with system 10.6 disk and can repair disk and Permissions. Still will not reboot like normal. I tried all the troubleshooting tips on the web. I am lost for new ideas, please share some.