sorry for necroposting but I think this is relevant.
So I think the issue here arises from the fact that the icon name and the program name differ in .desktop file.
For example, I have my own app I am developing and I wrote a .desktop file for it. At the start, my Exec line contained the path to the executable at /usr/bin and Icon line had a path to /usr/share/pixmaps/. However the name of the executable was slightly different than the icon name itself. The program, when installed, shows the icon in Whisker menu and if I put the shortcut file on desktop, however no icon was shown when the program was running, only that blank icon - white window thingy.
Once I named my icon exactly like my executable name the icon started showing in the window buttons plugin on xfce panel.
I've tested this with Skype and Slack which show their icons correctly when installed because as mentioned before, the entries in .desktop files for Exec= and Icon= lines have the same name. Then I proceded to rename those icons and as expected their icons no longer showed in window buttons.
I'm on Xubuntu 20.04.1, Xfce 4.14.3.
Hopefully this helps someone!