NHF – new heroes for Heroes V 3.1.

Ah, I see you already have specialists with "extra-expert" skills in your mod; that explains everything. By the way, is the "extra" skill granted through scripts, or can it be achieved using the standard in-game mechanics (by editing text files)?

It can be done without scripts. Also, if you move the "extra-expert" skill to the slot of a racial skill, then all four perks will be displayed (since racial skills have four perk slots). However, if the racial skill is acquired during hero leveling, it will be recorded in a slot intended for regular skills, which only has three perk slots. Consequently, when the hero gains a special ability, the same problem will occur – four perks won't fit into three slots, and one of them won't be displayed.