I have this problem too. I use Windows 8.1 Pro x64 (with Slovenian MUI) with Fences 2.11.
I did some tests and found out that right mouse click do the trick and show Fences and icons. I prepared short routine that simulate right mouse click (and also left click to hide showed popup menu) and i put it in start foldes, so it starts every time at start up and show Fences and icons on the desktop without "mouse right click".
But, this is not right solution. I did some checks and found out:
Windows registry (with Fences installed) has two entries where are settings related to "show desktop icon":
if "HideIcons" is set to 0 then icons will appear (is not hidden)
if "HideIcons" is set to 1 then icons will not appear (it is hidden)
if "QuickhideActive" is set to 0 then icons will appear (is not hidden)
if "QuickhideActive" is set to 1 then icons will not appear (it is hidden)
So, after restart Windows and login as a user, icon will not appear. If you do right mouse click on the desktop in short time after login, you could see explorers popup menu without Fences shell extension. You could click "View" and see that "Show desktop icon" is not confirmed and registry entry "HideIcons" is set to 1.
After next mouse action (click) desktop icon and fences appear. If you do the »right mouse click« on desktop when Fences is already on the desktop, you could see that Fences shell extension is loaded and showed in pop up menu. Now you could see menu with »Configure Fences« and also »View / Show Desktop Icons«; this is Fences extension. I use Windows 8.1 with Slovenian MUI and the differences between explorers pop menu (right ckick on desktop) with or without Fences is visible becouse of different languages (Explorer is in Slovene language, Fences is in english language).
Also registry value "HideIcons" is changed from 1 (hide icons on desktop) to 0 (show icons on desktop) after right mouse click.
I did every combination with Fences or Explorers setting »show/hide desktop icons« on logout and restart Windows and every time when Windows is restarted or user do logout/login, registry value
is set to 0 and desktop is without icons end Fences. I also tried this with different Fences settings but it did not solve the problem. It seems that, becouse of unknown reason, velue "HideIcons" is always set to 1 at Windows startup or users login.
I tried to change registry value »HideIcons« to »0« on startup with simply *.reg routine (start this routine immediately after Explorer startup and before Fences dll or exe start) but no success. It seems that some of Fences dll or exe files couse this problem.
So, for now i will stay with my »right mouse click« routine at start up to show desktop icons and wait for better solution.
Maybe someone have better solution to avoid missing icons problem.