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Upsamplers, DACs, jitter, shakes and analogue withdrawals, this is it.

Yep

This sounds like a software problem (I can deal with that part).

1. Data goes into the front of the buffer (buffer size is 1 to N words, larger buffers create a bigger latency before starting playback).
2. An average time between data in the buffer is maintained. Here we are using the timing from S/PDIF, but averaging it so as to provide a consistent time between words in the output stage (step 3 below).
3. We output data from the back of the buffer (once the buffer is full) at the rate we calculated in step 2. We are still dependent on the incoming data rate, but the jitter between words that we got from the input is removed and replaced with the average input rate for all the data currently in the buffer. Inter-word jitter is reduced to 1/N of the original jitter (almost zero, since even with a buffer of only 1 second N would be 44K).

Voila. S/PDIF with no jitter.


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