Offhand, try seeing what is expected to load on system start-up.
Go to Start-> Search -> msconfig
"Startup"
Don't be afraid to search for anything peculiar, but be wary of disabling something that may be of importance. Using this method, you may be able to identify rogue software. If you can still boot the system in safe mode and are seeing these issues, there is a good chance that the problem is in the registry.