What would happen is it would sometimes drop audio halfway through a clip, or else Sorenson would simply quit after encoding 3 or 4 clips. But the batching problem may be peculiar to the version of Sorenson that I have... I seem to remember reading that there was a bug related to it that was fixed in 4.1, and I think I have 4.0, so I should prolly upgrade.
We use the "watch folder" function quite a bit, though... we have a machine dedicated to encoding and when we finish editing a scene, we just start it copying over the network to the watched folder on the encoding machine and when it is copied, Sorenson starts right in on it... very handy and keeps our work flow moving. But you should definitely have gigabit Ethernet between all the machines if you're going to do that, as it will take forever if you're copying across a 100Mbit ethernet network.
