For each tray icon XEmbedSNIProxy is creating container window 32x32 in size. It is black with opaque set to 0 (fully transparent when compositor is enabled). All of these container windows are stacked below all windows, so normally you can't see them. On creation all container windows are created in top-left corner. When user clicks on the tray icon, container window is moved to the click location (to handle events correctly).
On KWin restart all windows are shuffled, usually KWin is able to restore ordering correctly, but for some reason not it this case. As a result black/transparent container windows are stacked above all other windows and panels.
To solve that, on KWin restart, XembedSNIProxy needs to iterate over all known container windows and stack them below again.