Problem with the door seal and the dealership

So I was driving with the radio off and every time the cab "flexed" at all from the normal road driving the door would make a creaking noise. If you listen to the radio you can't hear it, but since it was on my mind I took it in to have it checked out. The service tech rides with me and says he can hear it but doesn't know what it is. I reschedule to ride with the main service guy. We ride but the noise is gone this time (WTF?). 2 weeks go by and the noise comes back. I take it and the service tech main guy rides with me agains and says it is for sure the door seal. He says "off the record" since my truck was made in Mexico, it was shoddily built and he isn't surprised. He personally owns a 1999 tacoma. He says that he wants to replace the whole door seal but toyota wants to take the easy way out and bondo it up. So today they bondo up the door. 5 hours later and as i'm driving home, the sound is still there. I call them back and they say they will talk it over and figure out what to do. I'm not super pissed off (yet), but a little annoyed that they just had my truck for 5 hours today and the noise isn't gone. If they call me back and tell me they aren't going to replace the piece, then I am not going to be a happy camper, and I am a really easy going guy. Any thoughts?