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The remote may be faulty. I just had this happen to me a couple days ago. Most auto parts stores have a display now where you can press the buttons on the remote and a little light will flash if it's getting a signal out of the remote. I'd try this next because it's a free way to check the remote. Autozone had this display if I remember correctly.
I'd still check it like I was saying above. It's not going to cost you anything and they'll fail and still show a red LED. At least you can eliminate the remote/s as the problem.
Have you tried to reprogram them?