I tried again the firmware update using the virtual disk. Drag and drop using the folder explorer (OSX Finder) does not work well but copying it with a command line works every time (App note AN11305 says something about additional disk activity done by the explorer). It shouldn't be too difficult to automate it.
cp hello_world.bin /Volumes/CRP\ DISABLD/firmware.bin
And here is a small 3D print case I added to the repository. Next I will clean up the libraries.
Edit:
1. I added the above command as an external tool in lpcxpresso that also does automatic build. It works like a charm.
2. The RST and ISP button labels on the board are swapped. Will fix it in next revision.