First file uploaded for publishing is missing intermediary folder in query results

The first file uploaded for publishing is missing intermediary folder in query results from ModeShape. As an example if the attached xmi and cnd file are published in that order the xmi file will be missing a intermediary folder but the cnd file will be correct. Reverse the publishing order and the cnd file will be missing a folder but xmi will be complete.

The following is an example query results of ModeShape using Squirrel:

jcr_primaryType jcr_path
mode:root /
nt:folder /files
nt:folder /files/cnd
nt:file /files/cnd/OracleDdl.cnd
nt:resource /files/cnd/OracleDdl.cnd/jcr:content
nt:file /files/xmi/Products.xmi
nt:resource /files/xmi/Products.xmi/jcr:content
nt:unstructured /sequenced
nt:unstructured /sequenced/cnd
nt:unstructured /sequenced/cnd/cnd
nt:unstructured /sequenced/cnd/cnd/OracleDdl.cnd
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterClusterStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterDatabaseStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterDimensionStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterDiskgroupStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterFunctionStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterIndexStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterIndextypeStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterJavaStatement
nt:nodeType /sequenced/cnd/cnd/OracleDdl.cnd/oracleddl:alterMaterializedStatement