Hey StickyNote,
If you could post the drill files or the exported files (Gerbers). I can also check them out as I work for a proto-type board house in the USA.
Old_Gray mentioned a theory about the production house making changes based on the parts. I have never seen a board house care about what the part is and Gerber data has no information about the parts. So I do not see them fixing spacing issues as they don’t have time or know what you really wanted…
There is also the possibility that you hinted about, the board house scaled up the data. This could happen as they have to account for the manufacturing processes. If the job was treated as a multilayer or was on very thin material it would have to be scaled up.
(Scale factors are based on the Material type, thickness, copper weight, layer types (signal, plane, mixed) and mfg panel sizes. ) The goal is to get a correct finished size board in the end but mistakes do happen.
let me know if I can help.
DiodeDave