Hello,
Sorry to hear you are having trouble.
In the lack of technical support,
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Shame there isn't a proper support centre...
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We are always looking to improve so can you better define what you feel is 'proper' or what we 'lack' in terms of support- where have we failed to be precise?
This happened in fences 2 and it has happened in fences 3
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Without more information, but reading how you have seen something in both version, there might be a misunderstanding of how Fences works.
does anyone know why, after installing fences 2 and then 3 do I get icons placed on the desktop instead of in a so-called fence?
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As RND pointed out, even with Fences installed, icons will go to the desktop unless rules are set up to have them routed to specific Fences or you move them manually.
If I try to delete them I delete the entire folder! So it hasn't just created the icons ~ its MOVED the folders to the desktop.
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Fences does not, nor has it ever, 'created icons' it organizes and displays them that already exist or are created by you / other apps.
There are two types of Fences, regular ones that organize desktop icons:

The only way regular Fences will delete icons is if you tell it to:

The other type are Folder portals which will allow you to map a specific folder, on any of your drives, to the desktop for viewing and management including deletion and what I believe you to mean here:
If these icons are deleted the whole of that folder is also deleted.
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Here are also 2 good videos on how Fences is used and some of its features:
https://www.youtube.com/watch?v=Hln00a2b0WY
https://www.youtube.com/watch?v=uBkvz3Kovr0
Do let us know if this clears up some confusion.
Sean Drohan
Stardock Support Manager