Possibly fried the LM193 analog comparator at U24. Connecting -12V to pin 4 of connector A6P1 would connect -12V to the positive input of one of the comparators. The data sheet specifies that they're good to 36V but those would be positive voltages. Negative could definitely fry the IC.
LM193 datasheet:
http://www.ti.com/lit/ds/symlink/lm193.pdf