So I have a regular 21" monitor as my main (mon1), a 19" wide as my secondary (mon2.) Naturally they have different resolutions.
For the new version (3.1.5) with Taskbar on each Monitor I'm seeing the background of mon1 "inside" the toolbar on mon2. If I make a straight line across mon2 to mon1, it so happens that the part of the background I'm getting is exactly where the bottom of the monitor is physically located.
Unfortunately this is a bug in Windows Vista. It renders the wallpaper incorrectly behind the primary taskbar, using part of the wallpaper from the secondary display. This is corrected in Windows 7, but there isn't anything I can do about it in Windows Vista.
But... in previous versions it wasn't so... noticeable. I'm still using the same wallpapers. I mean the wallpaper duplication doesn't even make it across the bar, it stops where the chrome button is on the taskbar.
The DisplayFusion taskbar now supports Aero in Windows Vista as well, which may explain why it looks worse. Can you post a full resolution, full desktop screen shot so I can see the issue more clearly?
