Hi Thomas,
can you try (on a test installation) to install the modern GnuPG version over
the one in the working Gpg4win? And see about the differences?
You can then try to enable GPGME debugging to compare the cases, see https://www.gnupg.org/documentation/manuals/gpgme/Debugging.html
The next goal has to be instructions how to reproduce a problem like this in public (easily, if possible).
Have you tried any of the remaining SKS servers operating?
Regards
Bernhard