Why does the installer boot the program?
If you're like me, you didn't actually give the user an installer, just the executable.
A while back, I created a small program that did a staggered application start up for stuff in your startup folder. The Delayed Startup Application was pretty simple and had it's source code posted too. Martin Schray then took the application one set further and added in an installer and posted an online video on how to do it. Using Visual Studio 2005, this is remarkable easy. I suggest giving it a once over.