folder missing from lefthand tree

I have been using smartftp for years, but when it went over to version 3 I 'know' it gets confused if there are two folders with similar folder names sets in. Current and previous v3 subversions do this.

The latest 'bug' is I have /language, /libraries, /log folders in the tree in www/ on my web linux server (bluehost) BUT it just refuses to show 'libraries' folder ever.

The reason I say confused, is that I notice it tends to not diplay folders properly, if there is a subfolder elsewhere under www/ with the same folder set in.

For instance, I have a main joomla site in www/
and another one in www/aa_test/ with of course, a similar subfolder set

I'm not saying it does actually get confused of course.

But certainly I'm always missing JUST my /libaries folder from /www which is damned annoying. I know its there, otherwise my joomla site would go off! Th equivalent /libraries folder inside the /aa.. subfolder shows ok.

Any ideas how to fix these missing folder displays, by smartftp setup settings or something?