Uncle Buck--Most of the non
-Windows programs that start at boot on my PC are those in HK_Local_Machine\Software\Microsoft\Windows\CurrentVersion\Run
(or the HKCU equivalent). Only a couple are in the StartUp folder.
programs (system programs) are probably in the various .ini files, .sys files, .bat files, Services, etc. and I suspect should not be messed with. http://www.bleepingcomputer.com/forums/tutorial44.html
However, if you want to add a program to start at boot then the StartUp folder is probably as good a place as any to try putting a shortcut for it as PeteC has suggested. Or you can program a command to permit this.