When SOA-P is installed into directory that contains space, like "JBoss SOA" a new directory is created named "JBoss%20SOA" on the same. This directory contains a data directory wih BPEL H2 database data files, like

JBoss%20SOA/jboss-as/server/default/data/h2/BPELDB.h2.db

But the same file is created even in regular data directory. It seems that under this condition the database is created twice from two different points.

I'd say that these lines explains it
2013-01-16 08:34:57,712 INFO  [org.jboss.soa.bpel.runtime.db.H2Database] (main) jdbc:h2:file:/home/jpechane/releases/531%20ER3/jboss-as/server/default/data/h2/BPELDB;MVCC=true;LOCK_MODE=3;LOG=1;DB_CLOSE_ON_EXIT=FALSE
.
.
.
2013-01-16 08:35:07,097 INFO  [org.jboss.resource.deployers.RARDeployment] (main) Required license terms exist, view vfsfile:/home/jpechane/releases/531%20ER3/jboss-as/server/default/deploy/jboss-local-jdbc.rar/META-INF/ra.xml
2013-01-16 08:35:07,136 INFO  [org.jboss.resource.connectionmanager.ConnectionFactoryBindingService] (main) Bound ConnectionManager 'jboss.jca:service=DataSourceBinding,name=BPELDB' to JNDI name 'java:BPELDB'
2013-01-16 08:35:07,139 INFO  [org.jboss.resource.connectionmanager.ConnectionFactoryBindingService] (main) Bound ConnectionManager 'jboss.jca:service=DataSourceBinding,name=juddiDB' to JNDI name 'java:juddiDB'
2013-01-16 08:35:07,206 INFO  [org.jboss.internal.soa.esb.dependencies.DatabaseInitializer] (main) Initializing java:/juddiDB from listed sql files
2013-01-16 08:35:07,412 INFO  [org.jboss.soa.bpel.runtime.db.DatabaseInitializer] (main) Initializing java:/BPELDB from listed sql files