It seems there is an issue with syncing the hidden desktop.ini File using the current 2.4.0 or newer 2.4.1 Version of the Windows owncloud client software. During a couple of years we´re still using the same customized "sync-exclude.lst" file in the installation dir to prevent the desktop.ini from getting ignored.
The reason is, beause we are using a third party software called "Folder Marker" to colorize several Folders in sync directory itself.
I also checked the setting "sync hidden files" in OC Client, which worked so far, but not now.
Seems that the filetype is ignored by a hardcoded setting in the program itself?