levels do not exist when going optical on a jb3.
you need and svu-1 to monitor the levels, which are only adjusted by using the UA-5.
You can still monitor the levels on the jb3, but you're right, they can't be set by the Jb3. An SVU-1 is not necessary, rather it's a luxury from the weak meters that the jb3 provides, although I ran them for a year and a half and really had no problems with them, I defintiely got used to it.
The Input switch actually has nothing to do with this. The Input switch determines which input is sent to the USB output, not the S/PDIF outs.
This might be a stupid question, but is your UA-5 digi-modded? It's worth asking.
If so, try pushing that p48 button some more. Sometimes it takes a few hits to turn on.