I just got a Ruby, and was disapppointed to have a similar experience to what is documented above. For what it's worth, it really doesn't sound like any valve amp-based clipping or artefacts that I have ever heard. It's a harsh digital sound that happens at lower volume with transients—a harsh crackling when using strong attack on lower strings—but is also apparent from slightly higher volume levels and above even as notes fade out. With high gain the sound gets very fizzy.
It does vary with amp types, and I need to experiment a bit more with settings. I also have tried putting an EQ pedal in front of the Ruby to attenuate the input signal without having to resort to the guitar volume pot (So far I've used a Jazzmaster, so not the hottest pickups around). This gets rid of the sound somewhat, but it also means that I can only really work with fairly clean sounds. When I add some gain pedals to the mix I'm back to dealing with the harsh sound again. I'm a bit confused that the problem could be caused by hitting the input too hard, since I thought that hitting the front of an amp—whether 'real' or simulated—was supposed to push it to make it sound its best. I'm happy to learn what I'm missing!
I've read that gain staging for amp sims requires more care than with 'real' amps, but I'm struggling to find the sound I want—some grit—without also getting this harshness. I'm also very envious of the many people who are happily getting great sounds with no trouble. I would love to know their whole signal chain, especially what is going on at the start and the end (is the chain going to a DI, line isolator, what interface or DAW, headphones?).
If anyone has any other advice on gain staging for this or digital amps in general, I'd love to hear it!