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Have you used it the way described?
Stats / Skill Points / Change Morale:
Open the skill page of the character and press hotkey to add more.
You will need to close and open it again to see the value has updated.
Does this only happen for options NumPad4: Change Stat Points By 5 and NumPad5: Change Skill Points By 5 or in the editor Misc: Stat Points and Misc: Skill Points too?