Thanks for the suggestion Jennifer.
We have solved this using a different approach. Originally our annotation layer was included as a separate layer in a service that exposes a number of different layers; including the pipes we wanted annotating.
Trying to render the annotations in a FeatureLayer was failing so the solution has been to move the pipes and annotations into a separate service and render them both using an ArcGISDynamicMapServiceLayer. This renders the annotations perfectly.