And another one bites the dust! The problem with the offset pads in pcb turns out to be a damn translate in copper0 that wasn't in copper1. Getting rid of the translate fixes the problem when the zero is set to bottom of the board.
Raspberry Pi Zero_pcb_fixed_new_schem.fzpz (39.8 KB)
edit: The original part has incorrect spacing in the pcb svg. I must have copied (or not copied over) that file when I thought my new version didn't work last night because now the version that I had marked as broken works fine with the latest svg files.
Peter