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Try as I might, Windows can sometimes be VERY stubborn about letting a program bring other windows to the foreground, resulting in the taskbar button for the window flashing when S+ tells Windows to make the target window the foreground window.
If this happens, interacting with the S+ UI will resolve this annoyance. Simply right-clicking the tray icon and clicking away will allow S+ to bring windows to the foreground. I make the necessary API call to request permission from Windows to do this, but I think it only wants to let S+ if the user has interacted with a UI component at least once (to mitigate malicious apps from doing this). I could probably fix it permanently by having a S+ splash screen or something, but I hate splash screens and it doesn't happen often.