Derek responded to this in another thread.  The benefit is not applied until the following turn. 

I've seen this too, it is most easy to note with regeneration spell because you can see it tick.  My hero who has had the spell since turn one is only getting one life, my heroes who got it much later, before a big fight, are getting three.  Similar issue with amount of protection from stone skin spell.  For what it's worth, I think I noticed the same problem the other way; my  Stone Skin spells are still pretty strong, even though I later lost a few of my earth shards.

Clarification!  It seems that after saving and reloading, all my buff spells are getting nerfed to basic level, despite the fact that I have several shards, and had them at the time of casting for some (but not all) of those heroes.  Check out this save.

http://dl.dropbox.com/u/59263671/Bug%20reporting%20time.EleSav

I PROMISE that my sovereign has had those spells cast on her since the start of the game, but those other two buffed heroes had them cast much later, after I had several shards.  To test it further, feel free to cast the spells on another hero (I used the 4th one in my super stack), they will display the proper (powerful) values, but if you save, then load again, it resets to basic (shardless) values.

Horray, I responded to a blue!

That must be it then, the reloading of a saved game. I do tend to reload a lot to test different scenarios. Good find and thanks for the response Derek!