I worked on the enterprise side of the fence (SGI, NetApp, VMware) from 1998 to 2009. We always called them "users" there, too, even though they paid us gobs of money. We do this for the same reason manufacturers of hammers call their customers "customers" when they're buying and selling hammers, but call them "users" when they're using the tool, however they came to possess it. Software is a tool; the people using it are users.

"Customer" emphasizes the transactional side of the relationship. If your check bounces, or you pirated your copy, etc., you're no longer a "customer".