I observe the same bug on 5.0.0.CR2 and 4.3.10.Final
in that statement :
insert into DifferenceVersion ( volume,volumeVersionFrom,volumeVersionTo,parentFrom ) select :vol,:vvfrom,:vvto,dfrom from DirectoryVersion as dfrom where dfrom.volumeVersion=:vvfrom and not exists (select dto from DirectoryVersion dto where dto.volumeVersion=:vvto and dfrom.path=dto.path

I can give the annotated entities if it helps.