In a popup window for selecting files from upload folder, I have structure like this

Root
  |
  --> Upload
  |
  --> Root
        |
        --> Upload

I am using N2 built from GitHub on March 21st. Installation I am using contains two sites under one N2 tree.

I can't seem to reproduce this. Any other clues?

Sites are defined as following

	<sites>
		<add id="29" name="B2B" wildcards="true">
			<settings>
				<clear />
			</settings>
			<uploadFolders>
				<clear />
			</uploadFolders>
		</add>	
		<add id="50" name="Retail" wildcards="true">
			<settings>
				<clear />
			</settings>
			<uploadFolders>
				<clear />
			</uploadFolders>
		</add>		
	</sites>

Clearing config should be necessary in this case but shouldn't hurt either.

I did some changes to the upload functionality while adding support for permissions. It would be interesting to hear how these affects this problem.