Run
msconfig, look at the Startup tab, and if you see entries for Autohotkey (and other Startup folder items) duplicated with location listed as both "Startup" and "Common Startup" like this:
then the probable cause is that you
deleted the startup folder in your individual user startup menu. (This is a known bug in Windows XP.) Take a look at
C:\Documents and Settings\%username\Start Menu\Programs (where
%username is the username that you log on to Windows with). If there is no
Startup folder there, then you need to create a new empty folder named 'Startup'.
You may also need to edit the registry to undo the bit of Windows stupidity that happens when the user Startup folder gets deleted. Look for key name:
Code:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders
and check that the 'Startup' data has the following value:
Code:
%USERPROFILE%\Start Menu\Programs\Startup
(that is to say, it should say %USERPROFILE% to match the other entries there).