Rather than tweaking how often it shows up (because it’s one of the more fun events to find), consider changing how scrolls stack to make them less exponential.
Right now, if you have six scrolls of -0.1s, and sell them, you’ll get -0.1s, -0.2s, -0.4s, -0.8s, -1.6s, -3.2s, for a total of -6.3s. That’s fun, but pretty broken. ;)
As much fun as it was to play with, and as much as I hate to suggest nerfing it, you might consider instead capping it, so that using a scroll of cooldown when you have other scrolls of cooldown will upgrade the other scrolls as if they were bumped uncommon->epic->legendary, with a hard-cap at legendary (so a legendary scroll doesn’t get any better). That would provide some benefit to saving them up (which compensates for having to hold off on using them and hope for more scrolls, which requires luck), but would keep it from being exponential.