JDK: 1.8
Neo4j: 2.1.5 -  Embedded and then stand-alone to test the data

I'm using a program to insert a large amount of data to Neo4j. Because of 
memory limitations and sped limitations I usually have to do this in a few 
batches using BatchInserter (separate commands, long after the database has 
shut down -- not multiple threads). I'm getting things like this:

START x=node:main(id = "Medtr2125s0010")
  MATCH (x)-[:EXPRESSED]-(y)
WITH x,y
  MATCH (y)-[:EXPRESSED]-(g)
RETURN x.id,y.id,g.id

Results here (copy and paste from the Web Console wasn't pretty so this is 
by hand):
x.id: Medtr2125s0010
y.id: Nodule
g.id: PAC:26323170
Returned 1 row in 110 ms

Which doesn't make sense to me, not only should there be over 20,000 
entries, even if it is finding just this one it should find the same x.id 
where g.id is.
I've had no trouble doing multiple BatchInserter calls before, but have had 
lots of trouble with the 2.1.x line, I believe it is related to the 
RelationshipGroupStore, which was causing a massive slowdown (see my 
StackOverflow question here: 
http://stackoverflow.com/questions/26451609/relationshipgroupstore-mapped-memory-setting-for-batchinserter
 
).

I plan on trying only 1 BatchInserter incarnation tonight and running it to 
see if it finishes properly and will report back. But this seems like a bug.

Any advice on speeding up when RelationshipGroupStore slows down during the 
insert would also be greatly appreciated.

Thanks,
--Joseph

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