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There's a few anomalies with the current setup.
First, Sesame's memory store is truly stored in memory, and I access via both a custom app, and the standard REST interface. This produces concurrency issues, since the Sesame application stored for the REST interface doesn't seem to sync as often. Also, the console fails to catch this unless the url at http://localhost:8080/openrdf-sesame has its web container restarted.

These are all stored in memorystore.data. I plan to ask if sync is set to 0, how long does it take?
THe java app I wrote is transaction safe, but that's only against the memory store, not how often it pushes to file.

This is an interesting problem to have, better than not knowing what's going on.
I've posted a forum topic on this over at openrdf.org.