Airport IPv6 Router Advertisments?
Make sure your Airport Express is updated to the latest firmware. Up until recently the Airport Express would get an IPv6 address for itself but would not issue them via DCHP which is why you needed to do it manually. This may be what's happening for you. The Airport Extreme only gained DHCP support for this at the last firmware update so I'd assume the Express did too but I don't have a newer AE to know for use and the older model doesn't support IPv6 at all.