I have the same problem with Transmission.
Sorry for another mail, but I need to make another last correction:
It's not Transmission specific. A simple
$ cd /cygdrive/path/to/download/dir
$ touch test
will result in the same broken permissions for test.
Doing this in $HOME will result in these Windows permissions:
NULL SID
Everyone
<My User>
Nobody (actually non existent S-1-5-21-...)
There are also no warnings and no prompt to re-order permissions.
File permission for an older file (created before cygwin ACL changes):
Everyone
<My User>
Nobody (actually non existent S-1-5-21-...)
So the new ACL implementation simply messes up in directories with
non-cygwin permissions.
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