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I am also seeing this problem with Windows 10 and Fences 3.03. Looking at windows file explorer, the shortcuts still exist on the desktop. However, dropping them in a fence "hides" them. Very scary when you drop an icon and it disappears.
Yep, I have the same issue. It drives me crazy. Daily I am having to grab icons that have broken away from their fences (like lost little sheep) and putting them back in their corral. I have no idea what it causing it to happen. I was a long-time user of an older version of Fences. After upgrading to Windows 10 I upgraded my Fences. The issue started at that time. I never had a problem previously. Any help would be appreciated.