The solution to going from S/PDIF (optical or coax) to USB, is to have the first piece of music you play on USB use the same family as the last piece played on S/PDIF.
For example if your last piece on S/PDIF was 48KHz, play something at 48, 96, 192 etc on the USB. It doesn't have to be a full song, it can be a half second of tape hiss at the right sample rate. I would just keep two files handy, one at 44.1, one at 48, that you can play before anything else. As above they can be very short and soft so you don't even notice them.
The other issue can happen if the DAC is set to USB and you have something plugged into optical or coax and actually playing, when you switch over from USB to S/PDIF (optical or coax) you can get some weird sound for a little while. This should not happen if you don't have anything playing into optical or coax while the switch is set to USB.
John S.