v2.13.1 is quite a step up, looks fancy and working as charm,
except one strange thing - no pop-ups (i'm using official Kobocoin-2.13.1-win64)
Yes, it's definitely a step up. Kobocoin at Bitcoin core 0.13.0 is a major milestone.
I've been doing some extensive testing on it to make sure everyone's funds are safe. I haven't posted an update yet so I'm surprised you found it!

Which popups are you referring to? I've got a new wallet running on win64 and it seems to be responding. It's possible there's more tweaking to be done.