Posting this in case anyone else has a similar issue.
I found the issue (which I'd suspected was MIDI but feared was more serious) using a MIDI monitor tool. My NI Komplete Kontrol S61 was sending sporadic CC21 messages - which on the Virus Ti2 is the Key Follow parameter - and completely messing up the patch. So I've disabled the rotary on the S61 which was mapped (by default) to CC21 and the issue is fixed. What a relief!