The PC that is introducing the noise is not in this playback chain, it is the file server which is connected to the HTPC via gigabit ethernet and which serves media content to the HTPC. i.e. I can physically turn off the HTPC & the RME FF and put the Marantz prepro into standby but the noise remains. I haven't tried physically unplugging those devices though yet.
I would take some additional steps to isolate before I got too much farther down the road. I would start by unplugging the inputs to the sub amp (as in the rca or xlr input plugs), then unplugging the inputs to the marantz, then the fireface, etc. until the noise presents. I'd also test with everything on, but with the server's ethernet cable unplugged (or with the server entirely off). It would be unfortunate to spend a lot of time troubleshooting the server if it turned out that the noise was coming from a different source.
I say all this because if the server is only connected to the HTPC, and the noise continues with the HTPC entirely off, that makes me skeptical that the server is actually the problem (or suggests that the noise is propagating in an unusual way). It's possible, but I've never personally encountered (or heard of) noise propagating via ethernet, much less when intervening stages are not powered. So unless it's propagating via powerline or RF pickup (which is less common, but not impossible), the server seems like an unlikely candidate.
And if it is a powerline or RF issue, then you've got a completely different set of problems (my advice above would not help either one, although dean's advice might).
Severing the connection at various stages will tell you if the server is "communicating" through unusual channels.
I think, but am not certain, that the problem was introduced when I changed my gain structure to avoid the need to attenuate all the main channels digitally (to account for LFE) & instead I now raise that back up later in the analogue chain. The net result of this is that the gain dial on the sub amp is now about 8dB higher, i.e. the attenuation it applies on the front end is now smaller. This means the SW signal coming out of the RME/Marantz is now weaker than it was before given the same dBFS signal.
I'm not sure if this extra detail makes any of the suggestion more or less applicable here. It seems like restructuring gain, so that the signal is hotter into the amp, should do it but seems like it would be preferable to tackle the noise at the source instead.
I think that's significant as it suggests that the noise has likely been present previously, but inaudible. As for tackling the noise at its source, if it is the server, the way to tackle it will depend entirely on how it's propagating.