Server finder not showing all sub-folders

Question

When I access my Mountain Lion Server from my iMac, I instantly have access to folders and sub-folders. But on some (but not all) of these I cannot then access documents within them. In other words, in the multi-pane Finder window, the final pane is simply blank. i.e - Serverdata>Folder>Subfolder>Blank
Read/write permissions on all relevants docs and folders are identical and open for me as an admin. On the server itself, all folders, sub-folders and docs are clearly visible. I'm obviously doing something stupid....any ideas?!

Answer 1

I forgot to mention i've also made this "make shift" refresh button
tell application "Finder"
tell front window
update every item with necessity
end tell
end tell
Copy it, open Script Editor and save it as an executable application in your Utilities folder. Now put shortcuts to it in your Dock or your Sidebar or whereever. When you run it, the frontmost window in the Finder will be refreshed to its most current state from disk.
When I can see all items(when freshly mapped) and I click the app i've made above it removes the same files and folders from view.