When you copy or create files in Windows as a domain administrator, the files can have unusual ownership in Cygwin. The ownership appears as Administrators, which is a group and not a user. For these files and folders, only the first channel of a session (created by the domain administrator) has write permission. All the other channels within the same session receive a permission denied error.
This is expected behaviour for the limitations of OpenSSH in Cygwin. In SNC_SSH, every sftp command has its own ssh channel, and when the sftp command is finished, it closes the channel.
Copying or creating files in Windows as domain administrator causes the files to have the Administrators group ownership in Cygwin. For those files/folders, only the first OpenSSH channel opened by the domain administrator session has permission to write, all the other channels will get the permission denied error.
As a workaround, after copying or creating files in Windows, check the files in Cygwin and ensure they have the right ownership, always to a user, not to a group.