Account Monitor Reset and/or Directory Monitor Reset under Advanced Options allows you to clear alerts.
We will highlight this more clearly in the manual with the next update.

Thanks anyway I figured it out.. This program works great... Thanks

I think this is helpful however, I have the emails setup, but after the email is sent the notification does not clear, how do we clear notifications so we can see new ones... Thanks in advance

The lack of detail in the alerts is intentional, to keep information about the exact nature and origin of the detected event away from potential hackers. If you want to see the details, you can configure an email notification under Advanced Options. The email will tell you what the issue is. It will also help you to decide whether you want to exclude specific directories from being monitored.

I have two alerts that are completely useless because I don't know what the are referring to...

JHacker Watch plug-in: A file integrity issue has been detected.
JHacker Watch plug-in: A directory integrity issue has been detected.