Sometimes the Run command does not work. In that case, the ShellExecute API function is worth trying.

shellexecute.ahk

strFilePath := A_WinDir "\notepad.exe"
if (ErrorCode := ShellExecute(strFilePath)) <= 32
	msgbox % ErrorCode

ShellExecute(strFilePath, strArgs="", nShowCmd=1) {
	;http://msdn.microsoft.com/en-us/library/windows/desktop/bb762153%28v=vs.85%29.aspx
	HINSTANCE := DllCall(A_IsUnicode ? "shell32\ShellExecuteW" : "shell32\ShellExecuteA"
	   , ptr ? ptr : "uint", 0
	   , "uint", 0
	   , "str", strFilePath
	   , "str", strArgs  ; arguments
	   , "uint", 0
	   , "int", nShowCmd	; specifies how an application is to be displayed when it is opened
	   , ptr ? ptr : "uint" )
	Return HINSTANCE
}