I used to run the UA5>JB3...
You need power up the UA5, all set up with the way you want, before you power up the JB3. The JB3 wants to lock onto the incoming signal, but will only do so correctly if it powers on while recieving it. If you have the JB3 powered on, it defaults to 16/44 (methinks), and doesn't correct itself to whatever the UA5 is sending...
As for batteries, the external power wants to charge the internals before it powers the JB3. I always left both internals in, and kept the JB3 fully charged. I used a 12v SLA into the car-charger to run power for more than 5x hours and had very good success.
The JB3 will also freeze up if it loses its optical signal. Not sure it just doesn't keep going and leave a blank spot, but it just stops. I guess it assumes its the end of the "program". Anyways, if your UA5 power blinks, or the cable gets knocked around, it may cause the JB3 to freeze up.
Good luck!
Terry