After updating to quodlibet-2.2.1 with the integrated plugins package, I no longer get a tray icon. The plugin is enabled in the plugins window. Reproducible: Always Steps to Reproduce: 1. Start Quod Libet 2. Look for tray icon in system tray Actual Results: No tray icon appears in the system tray. Expected Results: An icon appears for Quod Libet in the system tray. Previously, the tray icon worked while it was a separate ebuild.
Works fine here, try wiping old configs from your home directory, and if it still doesn't work... provide some output.