I'm assuming that you re-scanned for new plug-ins and that you have the AF dongle plugged in to the same USB port that you initialised the programme with. I had AF working perfectly well in Sonar for about five minutes, then a key stuck on the virtual keyboard and all other functions ceased. I could, however, close the synth down and continue working in Sonar. Re-starting AF didn't start it working again - only starting a new session in Sonar. In all fairness, this isn't the first time I've had problems with Sonar and virtual instruments. I really need to perform a clean re-install but I don't use it enough to merit the time right now. Analog Factory works seamlessly in Project 5, Tracktion and Cubase for me. I still haven't experimented with it in Live or Pro Tools.
Sorry I can't help with your problem in Sonar. I don't understand why it works well in Project 5. Perhaps the products are not as similar (in handling VST's) as I thought.