This does not appear to be true, probably due to a bug. I DID unlock magic - then I looked at the inscription table. It already had recipes for arcane bolt. Thus, I put in the runes, but it didn't craft it. Later, I crafted it with a different recipe.
I got another spell, Fire Shield, but the runes for that one did not work either. I presume that with enough work, I could discover that the recipe is there, just not with the suggested runes.
Again, SMP and NEI.
Everything works fine in SSP, pretty much.