They are all standard links (no alternate icon) however other applications also with standard icons do show. Is there any way for Start11 to refresh its cache?
Start11 doesn't maintain any cache, it uses the OS ones. If you get the wrong icon the most likely explanation is the OS is giving Start11 the wrong one.
If you right click on the pinned shortcut, what icon appears in the popup jump list?
Also if you change OS scaling factor to another size, does the problem continue?