Currently when you select a drone chassis, it automatically populates a "DRONE Skill Unit" based on that chassis, which is presumably based on the "Bonus Skill Unit" listed on p. 75 of the core rulebook. However, the rules clearly state on p. 74 that the Bonus Skill Unit is "in addition to the skill gained via the drone's skill unit ability". PCGen currently populates the Skill Unit with the chassis' Bonus Skill Unit and leaves to room for the actual Skill Unit the player is supposed to choose.
FYI, including both character pcg file and that character's drone pcg file, since the drone does not seem to like it when opened as a file independently from itse mechanic.
Window 10, Ubuntu 17.10