Eclipse uses a modal dialog box (you know, those dialogs that you just HAVE to deal with before you can do anything else) to display the time and your graphics. This problem arises when another product tries to launch automatically while this modal dialog box is present. Some programs simply can't do this.
A way to work around this situation is to set Eclipse to "Just dim the screen" and not to have a password set. What happens is that Eclipse does not switch processes nor does it use a modal dialog box when it just dims the screen. This option will solve these compatibility problems.