Unfortunately, I do not have the Faderport. And there is no documentation how to work with it. I have created the preset for AZ Controller in cooperation with another user which had it. And it can happened something more should be done.
In other words, you problem is most probably not Sonar related, but my AZ Controller / Faderport mode related.
But lets check step by step:
1) when Sonar "does not see it", in the Sonar Preferences/MIDI, do you still see enabled Faderport MIDI ports?
2) you have registered FaderPort.dll, but it should not be used in parallel with AZ Controller. Open Sonar Preferences/Control Surfaces and check that you have either AZ Controller of Faderport, but not both
3) Faderport has different modes. If you use several DAWs, it is possible they are switching the mode (for already mentioned reason, I do not know how to do this from AZ Controller). To switch manually, press "Stop" and keep it pressed till "output"/"undo" start flashing (then documentation is unclear how the mode is indicated by these LEDs). Then press "OUTPUT" for one mode or "UNDO" for another. I do not know which mode you need, please try both.
I guess Studio One is switching Faderport into "correct" (for itself and AZ Controller) mode, that is why it always works afterwards.