Could you compare your icons to the standard ones in SVG? We usually do 4 icons for tool windows: 2 of 16x16 size and 2 of 20x20 size with some predefined colors. You can find source SVGs on the intellij-community repository
P.S. please avoid filled areas in tool window icons, they look out of place
I’m just replying for the benefit of any future readers. I ran into this issue too and spent way too much time trying to get icons to show properly.
To resolve the issue I had to manually edit and simplify the markup in my svg file to make it work. I am not exactly what combination of things resolved it, but it did start working for me. I removed clipping masks, expanded strokes, moved from style attributes to fill=“…”. etc.