Nexus user Asaforg, and I, has solved the Invisible Lightning/Shock Runes bug that some users have experienced. This bug is caused when a mod author places the wrong, special effects,projectile into to their mod with intent to apply a Lightning Rune Trap on ground cover. In the CK you will find two options within the object window under; special effect,projectile with the word lightning in the object windows filter. RuneLightningProjectile and TrapRuneLightningProjectile When these 2 projectiles are placed into the CK there is no telling the 2 projectiles apart, they look the same in the Ck and will act the same in created mods locations placement.The mod author clearly is not placing down the wrong one with intent.Had there been info on this prior for mod Authors, i would not be typing this now. What is conclusive is that the proper projectile to use,when placing rune traps on the floor is the "RuneLightning Trap", this is what Bethesda uses to place those rune traps. Any users that are suffering from Invisible Lightning Runes bug has a mod that has applied the -TrapRune Lightning Projectile - has a lightning rune to ground cover in that mod.
Edit:The other rune "traprunelightningprojectile" that was culprit in mods is now revealed to be what is supposed to be used on doors,gates,columns ect,ect. This is what Bethesda uses it for. I will stress again, when both trapruneslightningproject and runelightningprojectile are placed in a cell whilst in the ck the both look like the are the right one to go to the floor. As in they both come into screen on a horizontal plane.
FOR USERS SUFFERING: There is no easy way to know what mod is the culprit. Because we know that it is a mod that has placed a Lightning Runes incorrectly you can at least eliminate a large slew of mods in your load order. Until a reliable means for users,that are not CK users,is enacted you are going to have to apply the trial by elimination method.Your culprit mod is most likely a dungeon, cave,or expansive mod with new land.
After consideration, it is my opinion that trial by elimination is the best course of action to determine culprit mod for all users. I suggest starting a new game without mods that fall under the categories of Dungeons,Caves, and Expansive new lands.Make a clean save before you arrive to where you were experiencing the invisible lightning runes. After saving, go and make sure culprit mod is still not in load order. Then add 1-2 of the mods that had been left out and repeat steps until found. For users that want to play in the CK, you would have to load 1 mod at a time into CK and activate in cell window cells that particular mod had added then look in item window,within cell window, for traprunelightningprojectile which inside item window is classified as a projectile.