Hi rdiez,
first of all, let me say that I strongly advise using "mount -t cifs" for such kind of tasks like backups over rsync. GVfs is designed to be used over GIO API by GNOME applications. Fuse mount point provided by GVfs is a just limited fallback...
Back to your issue. GVfs doesn't have such cache and I am a bit confused what you did and where you see the file (is /home/rdiez/WindowsShares symlink to /run/user/[uid]/gvfs/?). It might be possible that the fuse daemon crashed and rsync write something in /run/user/[UID]/gvfs/smb... in the meantime. So, you can see some file written by rsync in fuse mountpoint, but the file doesn't exist in smb share...
I am convinced that /run/user... is not persistent across restarts, so you can try rebooting your system to fix this issue.
Regards