Hi All,
Just spoke to my Vectorworks Tech Service Support. The problem seems to be with the local mapping - if you're making adjustments, they show on the sheet layer, but revert in the PDF. I have been told that a fix should be coming with SP3. The other tip I was shown is if you right click on the hatch in question, the second last option says 'New Hatch from Locally Mapped Hatch'. Save it as new hatch with the scale attributes that your happy with. (hot tip, if you then delete the resource with the scale mapping you dont want you can replace all with the new one you just made) - PDF should then reflect your sheet layer.
SP3 is suppose to be out in a couple of days, but if your slow to update, or still having troubles, this option is good to create new favourites that don't need to be remapped.