I do think some context might help you solve your own question.

The Japanese committed these atrocities during occupation of territories they inherited during the course of war. To put it another way, the Japanese committed most of the atrocities you are talking about (especially with regards to the Chinese) not during actual combat maneuvers, but during the ensuing weeks and months following the conquest of an area. For instance, the majority of the Rape of Nanjing's events took place after the fall of the city, not during the battle for the city.

A lot of the rationale for the Japanese doing this was that the Chinese were lesser citizens in Japanese eyes. This also is true for the Japanese view of the Koreans (who were only fit to be farmers) and the Taiwanese who were fit to be colonized.

So, since the Japanese had no real history of colonization (and had even had their borders closed for centuries, excepting the Dutch, until Commodore Perry) they did not experience any occupation of areas. So, while war and cruelty might not have been an anomaly, it certainly wasn't a prevailing trend within the society.

The way the Japanese treated their prisoners of war during the Russo-Japanese war was actually exceptionally well, several Russian soldiers wrote home about how gentlemanly the Japanese were. This might fit with what /u/QskLogic said below about the Japanese viewing other East Asians as inferior the Japanese and Europeans as equals, if not superiors. During the Meiji era the Japanese (nobility, anyway) went absolutely crazy for European goods and styles, and even supported inter-marriages between Japanese and Europeans to bring white blood into the Japanese nation.

I've heard it argued that the least disiplinined and generally bad soldiers were used to guard pow camp, and this effected pow treatment. Is there any evidence for this?

Nobody so far has mentioned good old racism which seems to my study of the era as the predominant explanation for a lot of actions. We (the U.S.) admired the German people for their qualities and the occupation of them went quite well all things considered. Not so much with the Italians and Japanese. The Germans treated American and British POWs with decency but were atrocious to the Russians and all slavs in general.