I have installed and have the latest version of the FlightAware Windows 8 store app.
I log in, pull down one of my alerts, and proceed to modify the alert preferences.
I select “Meeting the flight” for all the alerts (e-mail, mobile, mobile push wp7, windows 8) and Save the alert.
I re-open the alert and all the items are set to “Operating the Flight”. Similarly, looking at the Alert on the My FlightAware website shows “Operating the Flight” for all the alerts. If I change it on the website to be ‘Meeting the Flight’ (as desired), then I run in to my other bug where the Windows 8 alert is removed. However after doing this, the Window 8 app correctly shows ‘Meeting the Flight’ as the options, but (as expected) doesn’t have the Windows 8 alert enabled.