Mail message appearing and then quickly disappearing

I keep seeing alerts for email messages pop up in the top right corner of my screen. They disappear before I can even see who they are from. When I check my inbox, there's nothing. Nothing in junk mail or any other folder either.
I am getting email alerts for the emails that do end up in my inbox, but these alerts that appear and then quickly disappear are driving me nuts. There are a few forums I'm a part of and other services I use like eBay that I am not receiving emails from at all (except password reset types of emails).
My guess is that Mail is deciding that these emails are junk and filtering them, but I have no idea where they are going or how to stop this.
Any ideas?

I'm not sure this will work, but try disabling Mail alerts in Notifications, log out/in, and then set them back up.

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