I also ran into this same problem where 'adapt create course' installs some of the dependencies, but misses other and requires running 'adapt install' to work correctly and eventually that even failed to work.

It got to the point when I ran 'adapt create course' core dependencies became missing (such as 'cookie-signature', 'fresh' and various karma extensions) and was apparent something horribly went wrong since adapt create would finish, but never gave the notification to change course directory or run grunt build/server. The only fix was to remove all global npm packages and start with re-installing node.js.

After the wiping the slate clean, I was able to build a few adapt courses normally before seeing the dependency issue again, which requires running 'adapt install' to solve.

System Win7.