OK Simon,
It would be interesting for you to note when you see any of your Flight ID's on the screen and write down which ones are not causing an alarm. This would discount any incorrect crew entry and might help to identify the problem. I find that if the aircraft is already on the screen, then I don't get an alert, but I do when the aircraft appears next time. I can simulate this by deselecting Process Hardware Flights or Get Flights from Network (depending on if you have Alerts activated for Network flights) and then the Alerts do pop up as the aircraft are 're-detected'. I'm sure that this is how it's supposed to work to prevent multiple alarms.
However, having just tried this with RYR5706, I didn't get an alert, so maybe it is a Beta 3.01 problem with Flight ID's - I'll have a play.
You could always go back to the release V2 of the software. If you didn't uninstall it when you installed the Beta software then this should just be a case of running V2.