Though that is true.. It wasn't in a particularly "professional" environment. Do you think it would be better to change the "Indie projects" stuff to "Hobby" or "Mod" projects? When sending my cover letter, though, I am making sure they get that I have worked mainly on hobby/mod projects.
But that's what they're all afraid of. It's what I'm afraid of. You'd be happy to have this as a hobby, which is the best thing ever. What grads want is for gamedev to be their day job, and playing games to be their hobby, I know that's definitely all I did while doing menial jobs for 3 years.