Keep Script running in INACTIVE window

How can I keep the script running if another window pops up?

the exact command would be appreciated. This is what I've tried
after the enter command. standard command prompt in windows fyi.

controlsend ("Windows Command Processor")
controlsend ("{Windows Command Processor}")




;Ronnie K.
;Par and Rar Removal
;12.27.2012
Send ("#r")
sleep (1000)
send ("cmd")
sleep (2000)
send ("{enter}")

SLEEP (2000)
send ("D:")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.RAR /S")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.PAR /S")
send ("{enter}")
SLEEP (2000)
send ("E:")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.RAR /S")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.PAR /S")
send ("{enter}")
SLEEP (2000)
send ("F:")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.RAR /S")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.PAR /S")
send ("{enter}")
SLEEP (2000)
send ("G:")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.RAR /S")
SLEEP (2000)
send ("{enter}")
SLEEP (2000)
SEND ("DEL *.PAR /S")
send ("{enter}")
SLEEP (5000)
SEND ("EXIT")
send ("{enter}")
SLEEP (2000)