Will this work with a subfolder install?

I have discover.wooster.edu setup as a subfolder Network. I have Multisite Analytics enabled for the network and each site sees a place to enter a GA code. I have had several users tell me that when they enter their URL (discover.wooster.edu/username) into Google to get an analytics code, they get an error saying that the URL is not valid. So will this work for a subfolder install or does it have to be a subdomain install?