Hi Roger,
There's a feature in FSUIPC that can disable these messages. I'm not sure if you need a registered version to do this, though, I'd guess that you'd need to register it for any of the advanced features.
The multiplayer labels can be changed through your ATC/AI settings. No idea why they have changed from your previous settings unless it's fresh install or you've made a large change to FS. Have you checked your FS9.cfg file? See if there have been any changes to this file recently. As regards not seeing all the aircraft, check your firewall/antivirus, router settings. They may have changed due to a patch or recent update.
Hope this helps.
Cheers!