The source of the problem is cour_get, conf_get, wit_get, and charm_get in person.gd combined with the +=. Whenever those 4 mental stats are retrieved via the setget variables rather than directly through the stats dictionary it returns the sum of the racial bonus and the base values. So the += in mentalup of slave_tab.gd, and any other similar code, will add the racial bonus to the values stored in the person. The mental stat getter functions were changed by Aric's mod in a dangerous way, and a lot of work would be needed to fix all cases.
Basically, when this code runs
person[mental] += 1
and mental is "cour", it is equivalent to
person.cour = floor(stats.cour_base + stats.cour_racial) + 1