This has been asked and fixed quite a couple of times. Just use the search engine on these forums. You will find your answer.
Hint: Slot allocation. RefSkill.
Actually, it is easy. You have to get known to the slotting of skills.
_RefSkills -> UI_SkillTab / UI_SkillPage / UI_SkillColumn / UI_SkillRow
E.g. with chinese skills
"0 0 0 0" (always start counting by zero "0", not "1") equals
First Tab (Weapon) / First Subtab (Bicheon) / First row / First skill slot in that row
"1 1 0 4" equals
Second Tab (Force) / Second Subtab (Lightning) / First row (imbues) / fifth imbue (Thunder Phoenix Force)
Your "Black gap" and wrong placing is just a slot issue.
For example, bichon has a row which ends on 7 and a skill slot count of total 5 skills (0 0 6 4), your new skill is on the same row, but wrong skill slot (0 0 6 6, instead of 0 0 6 5).
(Just a recap for people having the same issue. This is your simple fix - reallocating your skills simply with this trick, check for the latest existing counter)