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Alert Central 1.0.0 can not process email messages that are missing the plain text message part, so for instance, if you were to send an email using MS Outlook to an email account on your exchange server, Exchange server will be smart and know that it does not need to generate the plain text message part because it is going to another MS Outlook account. Alert Central reads and drops the message in this case.
The next service release of Alert Central will remedy this problem and process html text message parts as well.
There may be options on your mail server to configure the account alert central is polling from to always send the message as plain text.
Do We know when the next service release will be? If it will be soon we can just wait, if not we will have to come up with a workaround.