I ALWAYS use 48khz wav files. The clicks aren't in the audio file as when I play over the same material again there either aren't clicks or they aren't in the same spot. I have experienced this issue before but usually it was a bandwidth issue (playing back a ton of unrendered audio). Not this time.
I am feeding the output of Final Cut Pro to a Kona LHe. The AES output of the LHE is fed to a Behringer Ultramatch Pro that allows me to convert it to S/PDIF so I can use it with a conventional Yamaha AV Receiver and I am monitoring it through that.