I'm having the same thing happen. Emails are being removed by Alert Central, but it's not actually generating any alerts for them.
I've been testing with three sources. A camera, a UPS, and another program. All 3 are sending emails out, all the emails are being received, and after a moment they are all removed by Alert Central. Only the emails from the program are being turned into alerts; the camera and UPS are being ignored. I've tried routing them through different SMTP gateways, putting different from addresses on them. Nothing works. Alert Central just won't pay attention to emails form some sources.
Are there log files anywhere we can look at to see why Alert Central isn't doing anything with these messages?
_matt