I've had this problem with a few different versions of pymol (including the build I downloaded and compiled a few days ago). What happens is at random times I am suddenly unable to rotate and zoom in/out with the mouse. Instead the left mouse button draws a selection box and the right mouse button seems to change the depth of view. As far as I can tell I'm not telling pymol to change the mode, it just happens. The only way to get rotation back is to restart the computer, which is annoying to say the least! I am running Ubuntu 8.04 on a Dell PC.