It is an FBV Shortboard MkII. I have tried different patch cables, but as the pedal & cable worked on the other amp this rules them out. The FBV is not in the signal path & I would expect this to purely be for control, so it would need to introduce noise to the internals but without looking at the circuitry it's all just assumptions. If the PCB with the RJ45 is on the same PCB as the midi connector I could understand this, but it's not worth thinking about too much as like you say there could be many scenarios which introduce noise.
As expected Line 6 advised not to open up or attempt any mods and to try a firmware upgrade and factory reset. The firmware was already at v2.5 and I'd already tried a factory reset...this didn't change anything. Only other option now would be to check the amp in to a Line 6 approved service centre, which I don't want to have to do with a second hand amp I've just bought which was meant to be working.
I have managed to arrange a return through eBay, so I've sent the Amp back (InterParcel & UPS Premium works like a charm!) and bought a brand new one from Andertons in Guildford. Arrived in Edinburgh on Monday and everything works perfectly. No hum at all and sounds great....shame about all the unnecessary postage costs but that's the risk with buying 2nd hand goods I guess.
Thanks to the people who replied.