One fix. Download GloriousAutoPollingRate.exe below and drop it over your existing copy.
The tray icon survives an Explorer restart
If Explorer crashed or you restarted it, the icon vanished and never came back. The app carried on running and carried on switching your polling rate, just with no icon and no way to reach the menu short of ending it in Task Manager.
Explorer announces a rebuilt tray by broadcasting a message called TaskbarCreated, which is the cue to add the icon again. That was never handled here, and not by oversight: broadcasts only reach top level windows, and this was a message only window, which is the natural choice for a process with no interface. The window is now an ordinary top level window that simply never shows itself, so the message arrives and the icon comes back.
Verified by restarting Explorer against both builds. On v0.3.1 the icon is gone afterwards. On this one it is still there, with the correct tooltip and the right colour for whichever rate is live.
Nothing else changed. If your Explorer never crashes, v0.3.1 behaves identically and there is no need to hurry.