Keyless entry remote

I thank you for the programming instructions for my 99 4runner. I ordered a new transmitter off Ebay and saved close to $200 from my local dealer. However my problem now is that if I lock the vehicle w/ the transmitter and open the door w/ a key the alarm goes off. Is this normal? How do I program the security system to recognize both the remote and key?

i have the same problem can you help me?

mine does the same thing. ive found nothing on how to fix it. its sorta annoying but you get used to it.