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My guess is Qt 6.8.2 that still has the full old Chrome gpu code running is acting very differently than native Qt 6.9.0. See my recent posts on big changes in Qt 6.9.0 and gpu support.
As so why running the AppImage matters is that it must be leaving its Qt 6.8.2 libs in the ld library cache, and for some reason the qt 6.8.2 lib versions are being chosen over the qt 6.9.0 libs by regular Sigil.
Restarting or shutdown would empty the ld library cache. There are ways to flush and recreate the ld library cache you could try to see if they impact things the same way as a shutdown.
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