So I don't know how much the cutscenes not skipping correctly affects others but its been a real issue for me. Maybe 30-50% of all runs I start end early due to the cutscene just before the wolf re-fight not skipping. For whatever reason, if this cutscene isn't skipping, no other cutscene will be skippable at all until the game is fully closed (Alt-F4'ed). This issue will continue to persist across other save files too once the first cutscene doesn't skip correctly.
I have also noticed that even if the wolf re-fight cutscene does correctly skip, there is still some chance that any future cutscene becomes un-skippable (commonly the final cutscene just after the guider fight).
I have tested this a bit today and have found a potential workaround (no failures so far in about 13 tries):
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Play normally until just before the wolf re-fight cutscene trigger
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Disconnect controller (this will force the menu to open)
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Close menu with keyboard and jump into cutscene trigger
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The cutscene should be skippable with keyboard (hold enter or space)
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Plug controller back in and mash dialogue (it usually takes a couple secs before the controller connects and you gain control)
Overall this adds at least an extra 5-6 seconds to every run :/
Hopefully this is potentially helpful - here's hoping this gets fixed as well as the boatman soon!