Did you by chance update from 2.0-M06 to 2.0 final? Without rebuilding the 
label store? see 
http://blog.neo4j.org/2013/11/neo4j-200-rc1-final-preparations.html



what happens if you run:

> START g=node(*) WERE g:GROUP RETURN ID(g);


Caution: manual upgrade between milestones 
Data stores created with any previous milestone version can not be used with 
2.0.0-RC1 unless a manual upgrade is performed. This is due to incompatible 
changes made to the store files. Please proceed with caution, backing up your 
data before attempting to manually upgrade. 


Manual upgrade (only from 2.0.0-M06, and after you've backed up):
Cleanly shut down on the old version on Neo4j 2.0.0-M06
$ bin/neo4j stop
Navigate to the database directory
$ cd data/graph.db
Delete the label scan store (this is the critical part that has a new format). 
It will be recreated on startup.
$ rm -rf schema/label
Start with the new version of Neo4j 2.0.0-RC1
$ bin/neo4j start


Am 03.02.2014 um 17:52 schrieb Jorge Braz <[email protected]>:

> Hi there,
> 
> I have two different CYPHER queries, that i believe should return the save 
> result:
> 
> MATCH (g:GROUP) RETURN ID(g);
> START g=node(*) MATCH (g:GROUP) RETURN ID(g);
> 
> The first query should get all nodes that have the label GROUP, while the 
> second one should select all nodes and then
> match only the nodes that have the GROUP label.
> I guess that, in theory, the node IDs returned by both queries should be the 
> same. That's not whats happening.
> 
> neo4j-sh (0)$ PROFILE MATCH (g:GROUP) RETURN ID(g);
> ==> +-------+
> ==> | ID(g) |
> ==> +-------+
> ==> | 181   |
> ==> | 204   |
> ==> | 205   |
> ==> | 389   |
> ==> | 391   |
> ==> | 376   |
> ==> | 202   |
> ==> | 447   |
> ==> | 416   |
> ==> | 610   |
> ==> | 19173 |
> ==> | 393   |
> ==> | 19245 |
> ==> | 19301 |
> ==> | 19246 |
> ==> | 233   |
> ==> | 608   |
> ==> | 611   |
> ==> +-------+
> ==> 18 rows
> ==> 
> ==> ColumnFilter(symKeys=["g", "ID(g)"], returnItemNames=["ID(g)"], _rows=18, 
> _db_hits=0)
> ==> Extract(symKeys=["g"], exprKeys=["ID(g)"], _rows=18, _db_hits=0)
> ==>   Filter(pred="hasLabel(g:GROUP(18))", _rows=18, _db_hits=0)
> ==>     NodeByLabel(label="GROUP", identifier="g", _rows=18, _db_hits=0)
> 
> neo4j-sh (0)$ PROFILE START g=node(*) MATCH (g:GROUP) RETURN ID(g);
> ==> +-------+
> ==> | ID(g) |
> ==> +-------+
> ==> | 181   |
> ==> | 202   |
> ==> | 204   |
> ==> | 205   |
> ==> | 233   |
> ==> | 288   |
> ==> | 292   |
> ==> | 376   |
> ==> | 389   |
> ==> | 391   |
> ==> | 393   |
> ==> | 416   |
> ==> | 447   |
> ==> | 504   |
> ==> | 505   |
> ==> | 510   |
> ==> | 511   |
> ==> | 513   |
> ==> | 515   |
> ==> | 608   |
> ==> | 610   |
> ==> | 611   |
> ==> | 19173 |
> ==> | 19245 |
> ==> | 19246 |
> ==> | 19301 |
> ==> +-------+
> ==> 26 rows
> ==> 
> ==> ColumnFilter(symKeys=["g", "ID(g)"], returnItemNames=["ID(g)"], _rows=26, 
> _db_hits=0)
> ==> Extract(symKeys=["g"], exprKeys=["ID(g)"], _rows=26, _db_hits=0)
> ==>   Filter(pred="hasLabel(g:GROUP(18))", _rows=26, _db_hits=0)
> ==>     AllNodes(identifier="g", _rows=836, _db_hits=836)
> 
> Looking at the PROFILE result i can confirm that 26 nodes 
> "hasLabel(g:GROUP(18))" but only 18 return when "NodeByLabel(label="GROUP"".
> I'm trying to understand why this is happening but i'm stuck.
> 
> It might be important to mention that these nodes are also indexed in an 
> Index called "Group". I know that something wrong happened while creating the 
> "missing"
> 8 nodes, because they also weren't properly indexes on Group Index. But i was 
> able to fix it, forcing the nodes to be added to the index. But i'm not 
> really sure 
> how to force the nodes to be labeled, because if I ask for their LABELS(), 
> they return all the correct labels.
> 
> Do any of you guys have any suggestion on how should I try to tackle this 
> problem?
> 
> Thanks!
> 
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