I may have found the source of the problem. I suspect it's the subject line of the emails that is causing AC to drop them, as they are using UTF-8 Encoding. This is a known issue in SCOM SP1. Here is an example of a subject line that SCOM is generating:
MS Details here.
- You enable e-mail notification in a Microsoft System Center Operations Manager 2007 Service Pack 1 environment.
- In the e-mail notification options, you enable the Generate subject line with no encoding (use if notification e-mails contain malformed subject lines) option.
I will attempt to apply a hotfix from MS to see if this corrects the issue.