Can you clarify what you mean by startup? When Windows boots, the services are started and then the commands in the HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run, RunOnce and RunOnceEx registry keys are executed. When an individual user logs into Windows, a similar set of registry keys under HKEY_CURRENT_USER are executed. In addition to that, the login script (if configured) will be run. The contents of the Startup menu will also be executed.

The nature of the problems that you may experience differ depending on which part of the process you are trying to use.