There's a race condition in the ingest pipeline which means that spindle-generate may be invoked before updated graphs are available in the quad-store or cache.
Unfortunately, fixing this is likely going to involve splitting spindle-correlate into two steps: one which performs correlation, and another which updates the index state to mark items as dirty, i.e.:
Alternatively, it may be possible to perform a sparql-put immediately after the sparql-get process has retrieved the previous state of the graph.