I own a Variax 600 and a POD XT Live for about a year, and I know pretty much how to use both already. I made some custom tuning in Workbench, and it worked fine (a simple half-step detuning to Eb which is quite useful and it's not in the factory presets...). Saved it to some specific body/pickup model which I'd use it a little more, a Lester something (can't remember exactly which one). But I decided to try it with a Strat later, so I just changed stuff to make it a Strat - first the body then the pickup. When I replaced the Gibson pickup with a single coil (bridge position), immediately the tunning changed to something strange, like if the guitar was like a 12-string poorly tuned - not a perfect pitch 12-string though. You can hear the correct note (say the E 6th string) and some other note slightly detuned, not the Eb, something inbetween or even higher than the original string was (I can't detect which note), like if I had switched to any of the 12-string models which obviously I didn't.

It's not the "live" sound of my strings either, as I tried it with the amp quite loud and it's still there (will check with the headphones to get it more detailed). I tried with a different single coil pickup (a Rickenbacker, a Danelectro), and it had the same effect, the guitar sounds with some strange detuned note and not the tuning I made. I tried some other humbuckers and the same thing happened. When I put back the original pickup I had with the saved customized model, the artifact disappears and the guitar is back to the customized tuning with no glitches.

It also happened while creating other new tunings, because I tried to create a detuned Strat from scratch to see if it would fix the problem - when I used a humbucker, it sounded fine (with any body combination), but whenever I added a single coil, it was in the wrong tuning again. It happened not only with the Eb but with a lot of similar attempts like 1 and a half step detuning (like the one used in Nirvana's Heart Shaped Box). It also happened with the bemol and # presets at the top of the fretboard of the Workbench, when I used these the tuning wasn't a half step but it was this messed up version instead.

Until a month ago, everything was fine. I don't remember making any serious updates like firmwares or such.