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I didn't stack All of them, I just kinda used one when I needed a little power bump for the next level.  Then as I got towards like level 8 I sold them all.  

I'm not a game balancing expert, so my suggestion on a fix wouldn't really be worth much.  But at least at first glance, not upgrading scrolls with scrolls as you mentioned below seems like it would work at least.  Although the guy below's suggestion sounds pretty interesting too, pending some number crunching investigation probably.

I posted about this scroll stacking thing the other day but the post didn't show up.  I see that others have commented about it too, so I maybe I'm just repeating a known thing.  But just for a quick example, this is not an uncommon run for me with a few scriptoriums, I didn't even have the magic pen for this one.  Every item I have has the minimum 1 second cooldown (the stone face was 1.5)