I found a script at this blog post which looked quite promising. A few simple transformations of the file downloaded direct from IEEE, updates from the comments on the blogpost and it was ready to go. I added in the lines to copy the files to the correct locations in Ubuntu's implementation of Arpwatch.
Here is the updated script:
Here are the basic steps and commands to do it on a terminal session.
1.Create the script using nano (copy and paste the script above) into a file called update_mac_addresses and then run it.
2. Make it executable
chmod +x ~/update_mac_addresses.sh
3. Execute the script. Sudo is only needed to on the last step to copy to updated files to the right place in the files system.