The alerts are still stored in the alerts.ini file. The alerts.ini file may be in a different location than you expect though. If you're on a Windows 7 machine, or any machine where the program files directory is not writeable by your user account, then this file (and your pingplotter.ini file) will be store in your user profile instead - under the PingPlotter directory in appdata.
If you can't find this file, email our support team via the Help -> Email PingPlotter support... menu and that email will automatically tell us the path to that file and we can give you the details.
- Pete
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