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You didn't happen to dabble with the -DPKG_SYSTEM_PYTHON cmake option when compiling Sigil did you? Setting it to 1 would certainly cause what you're seeing. Otherwise, Sigil should be using the exact same python paths/modules that you just demonstrated were configured properly.
Or perhaps you used the -DPYTHON_LIBRARY (and/or -DPYTHON_INCLUDE_DIR, -DPYTHON_EXECUTABLE) cmake options to specify a different python than your standard one when initially configuring Sigil?
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