Thanks G0ULI,
The md5sum text file has data in in. 622 kb's of it. First few lines are:
8ca2ee644190f1188c7a9990a0b83a26 maps/00/cfg/Delphi/V1/MAN/cfg_customer_update.tar.gz
3da3f939c288663942cd7f5a4e7931aa maps/00/cfg/Delphi/V1/MAN/cfg_customer_update_version.xml
d08963780af7c9abd8a254d47183142e maps/00/cfg/Delphi/V1/VW/cfg_customer_update.tar.gz
60595a797c3c3bb21312596ac0332072 maps/00/cfg/Delphi/V1/VW/cfg_customer_update_version.xml
02b61ddddbde39fbc314a13c30347d90
From comparing the files on the original SD card to the data unpacked from the zip file there are some 'empty' folders. The folders that are empty (on the original) include data that is in the md5sum.txt file. (This includes my VIN which I had to enter on the website before I could download the maps)
I'm guessing is somehow the text file (or whatever) is supposed to be "run" and it transfers information into the generic maps folders. Since this doesn't happen the map files aren't recognised in the car.
Sorta of a bootstrap. But my Mac is deactivating the file from running.
I'm going to try and find someone with a PC that I can borrow and try and unpack it to the SD card that way.