The WM_CLASS of chromium is "chromium-browser" but the desktop file is named chromium-browser-chromium.desktop. Because of this docky (and possibly other docks) cannot match the window to the application. To solve this either rename the desktop file to chromium-browser.desktop to match the WM_CLASS or add the line StartupWMClass="chromium-browser" to the desktop file. Reproducible: Always
Fixed, thank you.