EDIT: From personal experience, I can also tell you that IP policies are less clear at the undergraduate level around here.
I was pretty sure this policy of students/academics own their own copyright but share in patents was the standard in United States higher education.
What you're describing sounds pretty similar to the way it works here, but the gross majority of full-time graduate students in engineering are employed by their universities (as "research assistants" or similar) and thus effectively waive their patent rights.
(FWIW, I think it's great for schools to share in patents which originate within them, but I would like to see students and staff be more well-informed on the subject, and commercialisation efforts which span beyond a single industry--I know of very few schools which have accomplished that.)
At the sime time, there are two different rights; copyright and "usage right" (not sure if that last thing is translated correctly), which means that you own the stuff you've created, but you can transfer the right of using it to someone else.
'Sadly though, due to concerns from my employer regarding intellectual property and similarities in projects I've worked on, I've been asked to take down the site.'
We have no way of assessing the validity of these concerns from what has been said. If the company feels the open source project contains work they have funded, and don't want to release, then it is their right to ask him to withdraw it.
Also, unless Nick is primarily driven by open source participation there's nothing to say they will eventually lose him.