I think this could turn to your advantage, though - this may open the door to some fancy spells that don't conform to vanilla spells, like a concentrated barrage of fireballs. Obviously, the way it's set up is that the journals should be used to delete or change custom spells (which I didn't realize when I first started crafting some spells), but this means that if a player ever loads a save from before they created any custom spell, the next spell they create (if it's different) might not behave properly. Likewise, if I created a concentration spell, quickloaded, and created a projectile spell, it would launch like a projectile spell, but the "projectile" would be a very brief spurt of flames instead of an actual projectile. It was actually pretty cool now that I think about it.
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So if I created Custom Spell 2 as a single-projectile, then loaded a previous save and created a new Custom Spell 2 as a concentration spell, it would fire like a concentration spell, but launch a series of projectiles - big ones, probably using the Flames particle effect instead of Firebolts. Try A > Get A > Reload, Try B > Get Clem > wut? > Reload, Try A > Git Gud > dafuq? > Try C > etc. I was following a test pattern that went something like this: It definitely explained why spells kept turning out differently from what I selected, without my being able to nail down the reason. So when I created a spell again, I think its effects got mixed in with the one which had previously been created in that slot, leading to some really. However, I noticed today that while doing so left me with no custom spells in my spell book upon quickload, they still showed up in the Spell Crafting journal. What I was doing was saving before I created a spell (Experimental version), then quickloading if I didn't like the result.
However, I think I've figured out why I was getting some strange results - save games. I apologize for my previous rambling post, I dropped into my idealistic way of thinking without remembering the reality that vanilla Skyrim's magic system is flawed by design, and that you have to work with what you've got.