I have been trying to think this problem through. Since I am not a programmer, it is a different area.
But you have an application's icon, for its .exe file using a placeholder in Windows Explorer. Since I believe Mike is correct about the icon normally being coded directly into the .exe, how could it go missing?
One thing you might try is to use the CTRL+Mouse Wheel to change the size of the icons in explorer. Maybe it will work at one size but not another.
If this makes no difference, then could the resource be in another location and not hard coded? If that was the case, if the path to that resource was incorrect, or somehow access was being denied to that resource, or the resource had been moved, perhaps that could cause a generic icon to appear.
I was also thinking if the Path variable was not set up correctly, perhaps it could have an effect.
A reinstall of the application, as Zvit has suggested, should correct the situation, or perhaps there is a repair option in the Programs and Features dialog.
If you don't get it straightened out, I will install the app and see if I can find anything.