Try this and see if the problem continues:
- Disable all mods--every last one!
- Start the game and load your current save
- Make a spell at the spellmaking altar, as normal.
- Go find a bed and sleep your character for at least a day.
- Check to see if the spell still exists and is castable.
- Save the game as a different save.
- Restart the game leaving all mods still disabled.
- Check to see if the spell still exists.
If everything is alright at this point (the spell(s)) still exist, exit the game and start enabling mods either one at a time or in small groups.. Start the game with your recent save and keep checking to see if the spell is gone. If so, you should be able to narrow down which mod is causing your issue.
Should that not work, for whatever reason (and enabling all the mods doesn't cause the spell to disappear), do this in reverse. That is, create a new spell and then sleep. Make a new save and then start removing mods, one by one (or in small groups), restarting and loading your recent save each time until you determine which mod is causing the problem.
Chances are you should be able to discover what is causing the problem--I'd start by enabling or disabling mods that deal with magic or the Arcane University in ANY way first, as you'll likely find one of those to be the culprit.
Beyond that, you're on your own. I couldn't guess what might cause the problem if you have no mods at all!
+20 Luck to you!