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The RBY damage issue seems to be (at least partially) caused by pressing the "suggested spread" button in the teambuilder:
Tinkering with it, I also ran into this oddity:
If I recall correctly, playing video games with cash prizes falls under gambling in Japan, which is strictly banned. So you can't say for sure how well the soft-ban will hold there if money was involved.
Pardon me if I'm wrong but... aren't there only 38 lv ups that are affected by growth percents? I assume you got the extra level from the class promotion, which gives a rigged boost that is independent from the growth percents.