As far as I can tell, the problem is only with shortcut files
I recently installed a program called MarkdownPad 2.
The filename is
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C:\Users\Public\Desktop\MarkdownPad 2.lnk
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"C:\Program Files (x86)\MarkdownPad\MarkdownPad2.exe"
There are several other shortcut files that also do not display.
Refreshing has no effect either.
And the non-displaying of the icons is persistent over restarts. I've had this problem in FC for years, actually.
But there are a few shortcuts that do show up in FC, and they are .lnk files too. But it seems the the problem stems mostly from shortcuts created by application setup installers.