Heh, Frederic,
It seems that its Lilypond's (www.lilypond.org) fault.

It registered its bin directory in the PATH variable, which seems to
contain a python.exe too.
So the result of:
>>>import sys; sys.executable
'D:\\Program Files\\LilyPond\\usr\\bin\\python.exe'

As for the instances of python24.dll, there are two:
one in system32 and one in inkscape's directory.

I 'fixed' it, by defining python's directory ahead of lilypond's. Now
the right executable is called.

Is there any other way instead of positioning in the PATH variable?

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