[CentOS] A *very* strange C 7 question

Ok, I've got a user, I just built him a C 7 machine. The new one has an
ATI card; the old had an NVidia card. I got it to use the radeon driver,
so it looks ok (he has a very wide screen). However... he has a program
that renders a molecule (which you see as many connected lines, in various
colors). However... it used to display it against a black background, and
suddenly, it's a transparent background, showing what's under that window.

Anyone got any ideas about that?

        mark