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I used to get that before and it somehow worked itself out I think. Or it might be one of those starter bugs that Eman fixed for me. I can't remember now. I know it pops up again occassionally but seems to fix itself. I would suggest putting in a ticket.
I use Putty and WinSCP to connect to my server, so using WinSCP to get to directories is basically like using FTP. As for putty, when you login with root you're in "root's directory", but if you mean the absolute bottom than just type in
cd /
and you should be in the bottom.
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"Doing nothing is very hard to do . . . you never know when you're finished." - Leslie Nielsen
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