Hello Junior,
Does the program run elevated?
If so, then that's why it will not run at startup. By default, Windows will not run elevated programs at startup for security reasons.
In this case, you could use the tutorial below as a workaround to create an elevated shortcut, then place the elevated shortcut in your Startup program to have it run elevated at startup without getting a UAC prompt.
Elevated Program Shortcut without UAC Prompt - Create - Windows 7 Help Forums
Hope this helps,
Shawn