Well, it looks like RIPng is broken in RouterOS, when using Vlan's on the interfaces. It has the dynamic routes within the RIPng section, but doesn't redistribute them to the kernel-routing space.
Yuk. No IGP for a while until that is fixed. I will look at the OSPFv3 stuff in the next days, but that needs extensive testing on both Quagga and Mikrotik side, before I'll deploy that.
Got a mail back, that they'll fix it in one of of the next versions.