If you have removed the check from Startup in Msconfig then something must be returning it at boot.
Have a look at some of these Registry Keys and other locations to see if you recognise any of the programs.
Windows XP Professional starts logon scripts, startup programs, and services referenced in these registry subkeys and folder locations:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Runonce
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\policies\Explorer\Run
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run
HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\Windows\Run
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunOnce
%systemdrive%\Documents and Settings\All Users\Start Menu\Programs\Startup
%systemdrive%\Documents and Settings\username\Start Menu\Programs\Startup
The last two might be a good candidate for re-inserting checks in Msconfig.
Also when you are altering settings in Hide Inactive Icons it may be necessary to temporarily make the user whose settings you are changing an Administrator in case the Registry permissions are set so the limited user doesn't have permission to alter them or get them to stick.
A program like Hi-Jack This would also give you a list of all starting software.
Hi-jack This! can be downloaded from: