Okay, I found a way how to narrow the list of mods that caused problem, finally.
You need to:
1. Know what element kills or damages you with invisible rune.
2. Know the name of the problem i.e. "traprunelightningprojectile" (change element to what caused problems)
3. Open xEdit and through editor id when you load all your plugins check the name
4. Check which mods this is referenced in
5. One by one eliminate mods that are referenced and load the problematic zone where you were exploding.
6. When the rune is no more triggering - you found the mod that was causing problems.
7. Open this mod in CK
8. Find the rune type again and check info, look in which modded location it is present.
9. Open it in Cell editor and delete - or if you know much more then me, change to the right type, and you good to go.
