I am using ownCloud Version 2.6.3 (build 13765).
I have a red cross created when I create a folder and upload files to it.
check the Activity Tab on your client in the settings menu to get more information
My guess is that this file could not be synched because of an error.
Can you create files and folders in the folder structure at the same place using the web interface?
Just want to determine whether it is actually a server and not a desktop problem.