simply said, if you made one custom spell off stormbolt and you copy that spell and create a new one, both of these spells are under the same "spell ID" which is storm bolt, regardless of what different effects,damage,stun etc you do, both spells will be "casted" at the same time.
The only solution to this is to only make a spell with a different ID, as with what the others have said "firebolt" or maybe "hurl boulder" for that matter.
Worst come to worst you can use channel and alter the skills via triggering