The empty folders matter for Mavis Beacon Teaches Typing

I was recently asked to deploy Mavis Beacon Teaches Typing (a classic typing instruction program) to a lab full of machines. Bizarrely enough, it includes a very deep folder structure with a lot of empty folders. My first attempt at the deployment was to unzip the whole deal, but I was using a program that loses empty folders when decompressing ZIPs. Mavis Beacon appeared to work, but after the first person to used it logged off, it started failing in strange ways for all users; it would ask for a license key or just hang at a black screen. When I finagled the deployment to keep the empty folders, it worked fine. Evidently, it uses them for storage but won't recreate them if they're missing.