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Originally Posted by DiapDealer
That's strange. The only explanation I can think of would be that you possibly have a portable version of Sigil installed somewhere else on that machine and the shortcuts and/or Open With context menu are pointed to different executables (which would have different preference directories).
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A very wild suggestion here. Sigil stores the version in which it was originally created in the OPF. Perhaps, and I know this is very unlikely, if this original version was before the clips that the newer clips don't show? A test might be is saving an old ePUB again and then restart Sigil with that ePUB.