I ran the underlying Server Job in standalone mode and it extracted all of the rows that I expected but in the Director Log the following message appeared
DSD_SendEvent.B:Error Starting run
Cmd = SH -c'ActivityCmd START -file MSEVENTS/20050520085304000'
Output = ERROR: Couldn't get I/O for the connection to: localhost.
ReturnCode = 1
Because this is finishing with a warning my whole process now stops - as said before I haven't changed any code so think it must be environmental.