I was actually going to post a topic about this a few days ago, just didn't get around to logging in until today, and I find out that someone else has already posted a topic about it! Anyway, I had a post all written up, so I figure this is as good a place as any to post it:
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Fences seems to want to reset the image on the second screen so that it starts in the upper left corner of the image rather than continuing from the main screen as it normally does when the background is set to tile.
Dual monitor wallpapers normally depend on the setting of the background to "tile" in order to flow properly from one screen onto the other. The only exception I have seen of this is nVidia's "span" mode which stretches your desktop (including the taskbar and background image) onto your second monitor. Here's a screenshot I took while using nVidia's desktop span feature.
Anyway, I came across this problem when I was trying to find a way to have a seperate desktop picture on a used LCD that I received and am now using as a second monitor. (My main monitor is a 19" CRT set at 1280x960 and the LCD is a 15" set at it's native 1024x768.)
The NVIDIA nView Desktop Manager has a feature that allows you to choose a seperate desktop picture for your second screen, but the method it uses is to resize and stitch the two photos together and save it as a seperate image file that it can use as a single desktop image. It then sets the image to tile so that it will flow onto the other screen. (The new image ends up as tall as largest resolution of the two screens and as wide as the two screen resolutions put side by side.) I also tried using another program called DesktopFusion, but it uses the same method so it had the same result.
Here's a snapshot of my desktop with Fences enabled, and one with Fences disabled. Both use the exact same image file for the background. As you can see, Fences is causing the position of the second screen's background to be reset. I'm not sure how deeply this behavior is embedded into Fences, but I certainly hope that it can be resolved.
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So there's my post. Hope it helps!