By default Windows hides certain files from being seen with Windows Explorer or My Computer. This is done to protect these files, which are usually system files, from accidentally being modified or deleted by the user. Unfortunately viruses, spyware, and hijackers often hide there files in this way making it hard to find them and then delete them.
Windows Safe Mode is a way of booting up your Windows operating system in order to run administrative and diagnostic tasks on your installation. When you boot into Safe Mode the operating system only loads the bare minimum of software that is required for the operating system to work. This mode of operating is designed to let you troubleshoot and run diagnostics on your computer. Windows Safe Mode loads a basic video drivers so your programs may look different than normal.
Many programs that you install are automatically run when you start your computer and load Windows. For the majority of cases, this type of behavior is fine. Unfortunately, there are programs that are not legitimate, such as spyware, hijackers, Trojans, worms, viruses, that load in this manner as well. It is therefore important that you check regularly your startup registry keys regularly. Windows does offer a program that will list programs that are automatically started from SOME of these locations. This program, Msconfig.exe, unfortunately, though, only lists programs from a limited amount of startup keys.