I just had a problem and figured out the solution and thought I would share.

Using ZEN 6.5 SP1a servers and clients. Windows XP and Windows 2000

I had a ZEN app that was periodically skipping all the files and
subfolders during the filecopy process.

Specifically I was using the Distribution Options Tab, Application
Files, and copying a whole "Directory" including subdirectories.

I figured out that if a file is in use within the folder to be copied
(in my case my excel documentation spreadsheet), ZEN will apparently
skip copying all the sub-folders and files within that folder. As soon
as I would close the excel document, ZEN would distribute the files
successfully. Weird.