I had this same problem when I was playing with sending SMS from the command line. It turned out that the problem had to do with the chatty process that was running at the same time, chatty appeared to think that it should take care of all messages, it was chatty that removed them. So, just kill chatty and the problem goes away. You might need to kill chatty a few times because there is some mechanism restarting chatty automatically, but at least for me it worked to kill chatty a couple of times, then the automatic thing gave up, and after that I could send SMS from the command line. You can check if chatty is running using for example this command: ps -A | grep chatty
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