The computer is out of the signal chain with the Transporter, because you can use it via Wi-Fi. There is absolutely ZERO difference in sound quality between Wi-Fi and TCP/IP though, and I get drop outs on Wi-Fi so I use an ethernet cable. Squeezebox Server sends over the raw PCM data to the Transporter, which is where it converts it to S/PDIF or AES. This is one of the main reasons why I use it, so that the computer is not in the chain.
OK lets try this again...where are your source files stored ?