Ageing Technology
I imagine the import routine puts the direct debit/standing order transactions into a single monolithic database that is latency/performance dependent on the server it runs on and/or the storage it uses. No doubt RBS have upped the server spec over the years, put the database on faster storage, but baulked at actually rewriting or modifiying the app to use a distributed database. It's a scale-up problem.
Investment from RBS probably means "we'll buy more hardware" not invest in staff who know how to write the application for the modern world.