How are you saving them? Does it involve Opus? e.g. Are you dragging from FineReader to Opus, or is FineReader doing everything?
If you turn off Preferences / File Operations / Copy Options / Automatically select newly copied files does it stop them being highlighted at all, or does that make no difference?
Is FineReader what is causing the Opus window to open as well? (Or causing Opus to switch to the folder you're saving into, depending on how Opus is configured.)
If you close all Opus windows and do the same thing, does an Opus window open then with all the files selected? (In other words, does it only go wrong if there's an Opus window already showing the folder in question?)
If you turn off Explorer Replacement (Preferences / Launching Opus / Explorer Replacement / Don't replace Explorer), what happens then? Presumably an Explorer window opens instead. If so, is everything selected, or is it similar to what you're seeing in Opus?