I just want to post this, in case it can help someone else in the future. I had this infuriating problem for too long, and after extensive searching, found no solution guide for it online, despite other people having similar problems. I did eventually figure out the cause of the problem, and how to solve it.
Skip down to the bottom of this post for the TLDR version.
So I was making a custom spell in the skyrim creation kit for my character, using vanilla magic effects. A quen style spell (ala the Witcher) for a Witcher character. However, I was having a problem with the custom spell not showing up in my spells menu in game. I would add them to my character using console commands, and the message would pop up as them having been added. Also via console commands, I would be able to remove them or equip them. So I know the spell existed in the game. It was just invisible in the spells menu.
I had different versions of the spell (with different or additional effects), with unique names and id's, and some of the quen spells would show, and others wouldn't show, in the spells menu.
So after much trial and error I discovered the problem. The quen spell I had that wouldn't show had many alchemical effects (which belong to no magic school) built into the spell, and only two alteration school spells (foremost among them being ironflesh).
There was at least one alchemical effect which cost the most magicka of all of the magic effects (lets say that cost 200, while the highest alteration effect only cost 180).
Now I found out that with a created spell, in game the spell will only display in the spells menu if it belongs to a magic school. And the way the game decides which magic school to assign to is based on which magic effect costs the most magicka. So for example, if you have a custom quen spell which consists of two magic effects. One, iron flesh, belonging to the alteration school and costing 100 magicka. And a second, lightning cloak, an adept level spell belonging to the destruction school, and costing 200 magicka. The game will assign that spell to the school of destruction, and say it is an adept rank spell. That again, is because lightning cloak was the magic effect in the quen spell that consumed the highest amount of magicka.
Now lets say you add an additional effect to that quen spell, fire resistance. This fire resistance costs 300 magicka. Additionally, it is an alchemical effect, and so doesn't belong to a magic school. In that case, the game will assign that quen spell to no school of magic, and the spell will not show in your spells menu in game, even if added via console commands.
To fix that problem, just make sure that a magic effect belonging to a school of magic consumes the most magicka in that spell.
Problem: Created spell won't show up in the in game spells menu.
Cause: Game has not assigned custom spell to a school of magic, because a magic effect that is not in a school of magic (ex. alchemical effects) consumes the most magicka in that spell.
Solution: Edit the magic effects in the spell so that a magic effect belonging to a school of magic has the highest magicka cost in that spell.
Edited by jackedfridge123, 18 September 2017 - 06:38 AM.