if(!file.exits())
{
if(createHierarchy(file))

incorrectly calls the expensive (because synchronized) createHierarchy method in the common case where the file does not exist (because it's a uniq named new tx record) but the directory hierarchy does (because it's the create-once hashed dir tree). This causes excessive contention on the FileSystemStore instance object monitor lock. Should probably be something more like

if(!file.getParent().exists())
{
if(createHierarchy(file))