Ditch the microfiber cloth, they scratch.
Planet Waves 100% cotton cloths are what I use.
Actually, I've done tests with the soft towel-like microfiber cloths (not the ones that are flat like eyeglass cleaning cloths) and soft cotton cloths, and various polishes -- I was once into car shows, etc., and it was important not to have scratches and swirl marks from polishing. So I learned this stuff. Here are the microfiber cloths I recommend, and they do not scratch:
http://www.griotsgarage.com/product/micro+fiber+speed+shine+cloths+set+of+3.do?sortby=ourPicks
Paints are various forms of plastic coatings. Take a clear piece of plastic like a CD case, that scratches easily, and rub it hard with both the cotton and microfiber cloths. You will see that the cotton scratches the plastic quite a bit more. That's because the fibers themselves are harder and shorter.
The V12 finish is definitely more like the old nitro in that it's easy to create polishing scratches and swirls. The older poly finishes are probably harder.
Any true polish - as opposed to the PRS Cleaner, which is more of a quick-shine kind of deal that doesn't scratch - works by combining abrasives with a surfactant. As you rub, the abrasives break down into finer and finer particles, and as they do so, the scratches become smaller and smaller until the surface appears shiny. But these abrasive polishes aren't really daily cleaner kind of things. They're there to remove scratches or restore a damaged finish. Correctly used, with a light, fast touch and a decent amount of time and elbow grease, they do a nice job. But they're for occasional use. If the guitar is dirty from being played, the best solution is a damp (not drippy-wet) microfiber cloth to remove the dirt, and then a light dry with a clean one.
Like anything else, polishing is a skill - it seems bonehead simple, but it really involves some knowledge, the right tools, etc. I'm sure the guys who polish PRS finishes to look like glass would agree.
Every so often, the Cleaner can work like a speed shine or coat of wax, but I don't find that necessary very often. I do use it from time to time.
My 2011 V-12 finish is still new looking after two years of daily use. So it can be done with a little forethought and information. I also keep the guitar cased when not in use, which seems to me to be common sense to avoid accidents, kids, pets, and the humidity and temperature changes that occur over the course of a 24 hour period in every home.
If the finish is cracked, it may be a warranty repair, get in touch with PRS' customer service folks or your dealer!