I'm currently looking into this:
http://matznermatzner.de/en/bernd/2013/12/loading-non-amd-modules-requirejs-part-2-zurb-foundation/
It seems that the way Foundation integrates has changed slightly from older versions, which is why updating Foundation in the existing yeoman-foundation generator prevents it from working.
It may be that you're missing the:
{exports: 'Foundation'}
from the shim... will test this out soon!