I have two monitors on one machine (Ubuntu 14.04, Classic Gnome), one placed vertical (secondary), the other one horizontal (main monitor, where JD is). With JD1, whenever some dialog (information, confirmation, captcha, etc) has to be displayed, it was shown over the main window.

With JD2 (same desktop environment), dialogs are displayed all over the place, sometimes over the main window, sometimes on the same monitor beside/below main window, but most of the time on different locations on secondary monitor (all the way up, all the way down, around middle, etc). As both monitors are 24", hunting for dialogs isn't my favorite game. Is there any chance to always display them over the main window?

My second machine is headless Linux server, where JD2 is displayed on separate workspace, so no trouble there

Again, thanks to developers for JD2!