They aren't related to version 5, if you installed avast 6 over avast 5 as it will retain much of the infrastructure (folders) otherwise it would require a huge modification to the registry changing all the folder locations, etc.
If you dis a clean install of avast 6 then your folder structure wouldn't be C:\Program Files\Alwil Software\Avast5\def\ but C:\Program Files\Avast Software\Avast\def\
Avast isn't saying it doesn't recognise them as it own, but that it can't find them as the avast housekeeping has cleared out old virus definitions folders to keep hard disk space used under control.