Any latency? For example, if you are inputing a piano part, does the sound (which is now the output of the digital patchbay) "speak" as it should when the keys are depressed? Currently, without a patchbay, if I run optical out of computer #1 and the into computer #2, then merge and send out the combined signal, the parts from computer #1 are slightly behind. I'm hoping that this will not be the case when merging the audio via the Z System unit.
The latency that you mention is probably as a result of your audio card. Putting a digital patchbay between computers will still mean that you have latency because you haven't dealt with it at the source. You may try playing with the buffers on your audio card in the control panel in order to get the latency down. What kind of audio card are you using?