@stephenw10 Hi fella, thanks for the further suggestions.
Good news, I got it fixed. As per your (earlier) suggestion I started playing with the BIOS settings and I had also emailed PONDESK support in parallel. I actually got a reply from them with the fix about 1 minute after I had found it by accident (i.e. by trial and error), so at least they confirmed what I found.
The fix is to go here in the BIOS and disable the following:
Advanced -> IT8613 Super IO Configuration -> CIR Controller Configuration -> CIR Controller = Disabled
They said they'd made a recent change to the BIOS which had caused this and will be addressing it in the next update (I'm not sure how, perhaps setting the default to be disabled).
BTW, I did a quick Google and apparently CIR is Consumer Infrared, so nothing I will miss for my use case.
Thanks for your help on this, it was most appreciated.