This issue seemed to start with Fences version 3. I had Fences 2 and windows 8.1 and it was never an issue to have files on the desktop and save them. It is not reasonable to expect people to create a shortcut for every document they have on their desktop as a workaround. Some people have a lot of documents. And the purpose of Fences is to organize the documents!
This issue is related to the "feature" to "Place all new icons in this Fence by default". I have a Document fence and a New Icons fence which is where I have all new icons place. What happens to me is when Microsoft Word documents are saved, they apparently create a new temporary file. I can see the temporary file appear briefly in the New Icons fence, then when the save is complete, the document moves from the Documents fence to the New Icons fence.
Please Stardock! Fix this bad behavior or at least allow us to turn off that "feature" so it worked as before. Using shortcuts is not an acceptable answer in my opinion.
For those that are struggling with this, what I have done is to make new icons appear in the Document fence by default, then I move them out to the New Icons fence manually. This is much easier to manage than creating shortcuts to hundreds of documents.
I have used Fences for many years and really do like it. But this is one very annoying bug!