That's good. The folders with underscores do not display. However, when I click on a folder to view the contents in File Browser, I am taken to the first folder that shows up alphabetically on my server.
For example:
When I click on folder filename1, I'm showed the contents of folder _anotherfilename1. When I click on folder filename2, I'm showed the contents of folder _anotherfilename2...etc.
That's wierd. I'll have to test it when I have time.
In the meantime, try this:
rather than adding underscores to your folder names, just change them to regular folder names and then add the ones you want hidden to the HideFiles parameter in your _config.xml. I bet that will do what you want.