I don't know what that is. I usually use Object/Transform, and a box appears on the side, Then I select Scale.
I've noticed that missaligment thing on some parts but havn't bothered chasing it down. It might be due to boarder origin of the part, when you resize page to drawing, not being the correct distance from the contacts.
Open Inkscape EDIT/XML Editor and look at the structure of the original part.
Try to not hack the dir files, just save as new part, Export, unzip, then load the modified svg back into the new saved part with Edit.