When I was a lower level, lets say like 30, i had a 39% spear skill force magatama. and a 23% spear skill force magatama. Both added attack points. Over levels the attack points from the magatamas started to fade (lower). Eventually the 39% didn't add any attack points so i unequipped it. Now im level 47 and the 23% mag lowered the attack points to a point where's it close to being useless.
Can someone explain this?

Did you change your skills? If the maga say:
"+X Skill Force Y%"
That mean only Skills with Rank X and above can have the bonus skill force.
Another thing, the bonus dmg from skill force is hidden and never show in your Status. If your attack (number in Status menu) went up by equiping that mag, it's probably something else.

The rank minimum for the magatamas were 2+ and 4+ and my skills have always been above that

have you met the conditons of the magatama to activate?
Like:
if remaining HP: X% or more, Rank X+ (insert weapon type) Skill Force +X%
if (insert element) X or more, Rank X+ (insert weapon type) Skill Force +X%
if (insert stat) X or more, Rank X+ (insert weapon type) Skill Force +X%


example:
Gemini Magatama
If Remaining HP: 50% or more, Rank 4+ Spear Skill Force +39%

Yeah they're If 50% Health or more mags