Reference architectures are associated with specific domains - such as building bridges, roads, cars, airplanes etc. They are time tested, refined well documented, well understood and repeatable ways of getting things done. Such architectures normally outline the end-to-end processes, engineering strategies and specify all the relevant artifacts and configurations.
Specifically in the context of Software Architectures, reference architectures outline the repertoire of services, hardware, software and standards for end-to-end system implementation. Checkout
Sun's reference architecture for banking specs.
A flexible reference architecture is one that lends itself to a high degree of configurability and operates within fewer constraints. Such architectures often provide alternative design strategies and allows the architects to perform tradeoff analysis while chosing one varient over the other. For instance, for a system based on J2EE architecture, the architect can chose whether or not to use entity beans based on system requirements rather than what is dictated by the architecture.
Hope that is clear( as mud :roll: )