I have found a fix from Microsoft to try (It found just one issue, not sure if it was related to my problem)
called Common System Maintenance Tasks
http://support.microsoft.com/gp/system_maintenance_for_windows
What it fixes...
* Problems with desktop shortcuts and icons
o Shortcuts on the desktop don't work or are broken
o Desktop icons are broken or have not been used in 3 months
o Startup items don't work or are broken
I also found that Internet Explorer had the Alot toolbar, I went to Add Remove programs and uninstalled the Alot toolbar.