n3rd4i: Duokan is horribly under-documented. Especially their jailbreak (probably they just took Nilujes), their startup hooks and the list of modifications they make.
That said, what you describe sound like out-of-memory conditions. RAM, not flash. For everything you described I would have chosen one of the following two options (instead of messing with Launchpad): SSH into the K3 and analyse (hacker's choice) or power-cycle (layman's choice in order to get things done and going on again).
Also remember that you can always restore a messed up Kindle with ATK/k3flasher (I suggest Kubrick now). Maybe you should do so after that big party in your rootfs...