Are you using the RAVE Audio Mixer in Ultra to do the AFV and Mixing of Audio?
If you are just using the "pass through" of the audio on the source and not using the RAVE Mixer then you will only get the audio of the source that is on the Bkgd Bus of the switcher..
Sources that go into FrameSyncs would also then have them stripped since you would not be running the Sample Rate Conversion mode either.
Wiring diagrams and image examples of what the output looks like when the audio is not present would help here but my guess is that you do a Squeeze back or a BOX effect in the Ultra and thus the Server video is not on the BKGD but rather in a Key which means that you don't have audio since you would not be using the RAVE Audio mixer option.
#Carbonite