Another update, but first off, apologies if these posts are long and arduous. I just hoped to document my research in case anyone else came across the same issues.
I did some more tests. And I was too hasty to claim victory using an old laptop. What I found is that the Virus is still going out of time but appears to be pitching the arp to adjust for it. Instead of a sudden click/pop when synchronisation is lost, the timing discrepancy is compensated by adjusting pitch. This shoots a hole in my theory that it may have been caused by Logic X. To add to this I boot camped into Windows 10 and installed Ableton 10. Same issue occurs. This all begs the question, is it my Virus? The evidence is mounting that it is. I'm sure this isn't news to many, as I've personally read years of some peoples issues. That's not to say all have an issue, but there's enough anecdotal info to suggest that a fair number do.
The next thing I asked, is what would cause this. Is it the USB cable/connection. I've tried too many cables and hubs/ports that it's inconceivable that all of these are an issue, across multiple machines and OSes too. Then I came up with the theory that it is a DSP issue. Maybe there is some internal synchronisation issue between the DSPs. As a result I did a timing test, to see how often this happens and it's reproducibility.
Using a stopwatch and a repeating arp pattern with a reverb/delay clocked to the tempo I recorded when this occurred. On average at 44.1 kHz the clicking/popping happened every 136 seconds. It may have been 134 to 138 to account for my margin of error. At 48 kHz this reduced to about 65 seconds. The interesting thing is that this "clock" is occurring regardless of when anything plays. I say this as when I first play the sequence the timing varies on the first run (as I am catching this timing cycle at various points). From then on it is quite frequent and predictable. I don't believe these numbers are fixed, I think they are dynamic depending on the setup. I also noticed that at times I could initiate more clicks/pops by twisting knobs and adjusting parameters. And that is where I began to feel that this is caused by possible DSP load balancing or a DSP problem, as this is a predictable but also dynamic problem. My TI has always had clicks on the external ins too.
After all this I got to the point where I've had to finally accept that my Virus is never going to work as reliably as I wish it would in TI mode. For more than a decade I have lived with this pain in the butt problem. I know I'm not the only one, but it still grinds. Moving forward and what to do about it I'm split.
Should I just keep it and run it as a hardware synth (sensible!)?
Buy a brand new one/buy another off eBay and compare this issue to determine if mine has a hardware issue or not? If so, cut my losses and use the new one, if it's the same - return it...