After discovering what the Flawed perk did, I set out to optimize it by keeping positive flaws from appearing while weeding out those I did not want and rejecting them. With only a few more before I was ready to take Flawed and let the positive ones I had avoided go through, it seems that most flaws are no longer triggering.

Specifically, the Overprepared and Treacherous flaws, which previously required dedicated effort to avoid, now will not appear no matter how I try to activate them. I am reasonably confident that I have reloaded a save properly every time these flaws appeared, which should leave them in the pool. Others that are not appearing include Luddite, Bibliomania, and Dangerously Curious, though I was trying to get these so that I could reject them.

*Spoilers* For posterity, I completed the N-Ray Range to see if the N-Radiated flaw would trigger, and it did. This one may be special, though, on account of activating upon completing a scripted event. Anyway, hopefully some light can be shed. Is it intentional that the game caps out on giving flaws after a certain number are offered? Is this a bug causing these not to appear? I would greatly appreciate thoughts, ideas, information.

As an update, each of these flaws has since appeared. Sorry, all, but it seems that it really was just happenstance that they appeared incredibly commonly early on and then took many hours once I actually wanted them.