Had a colleague today that had a small rsync script that synced a local folder to a network share. Since he upgraded to OS X 10.9 all the files synced to the network share got the hidden flag set, so the files became invisible. First I thought it was rsync that made some strange things to the files, but after some testing I found out that if you mapped the network share through smb1 (cifs://) and not smb2 (smb://) the sync worked as expected!
Apples implementation of smb2 seems a bit unstable. This is not the first problem we experience with smb2 on OS X 10.9.