Small addition to your information. Member Kirshz over at the ulmf forums confirmed with screenshots that the missing card in stage 6-6 has now been filled with the new SR Runa Kamiwano, making it two SR cards in the pool for that area. Its probably safe to assume that it has filled the spot for 6-1 through 6-6 as of today's update.

Ah, and you put 2015-05-29 for the update when you meant 06-29

Edit: Confirming that pulling a lvl 100 card in Chance Time now levels a separate card rather than give Pero. I haven't had it happen for about a week now and the last time it gave me Pero. Had four instances today: 1. A Normal leveling a Normal 2. A Normal leveling a Rare 3. A Rare leveling a Rare 4. A Rare leveling an SR