I got a sample course for testing the signup process with WooCommerce. Everything seems to go well except for the students are being enrolled into the course. If you would you try it out, here is what you'll need:
-Coupon code for 100% off: WPMUCOUPON
-I've enabled WPMU support access as well
Just an FYI, I first tested this process with MarketPress and then switched to try it with WooCommerce. MarketPress isn't installed right now but CoursePress keeps pushing notifications to install it. Not sure if that is helpful, but it doesn't hurt to include more info!
Thanks for your time!