Do you have more info on your setup? What guide did you follow?
Also, are you sure it's not 1 of the following 2:
1. you set the ftp user root to / instead of /path/to/clients/clientx/webx/
2. you have Jailkit enabled, in which case, you will see etc, var, usr and the rest, except they're in fact copies put in there to allow Jailkit to work... (see http://www.howtoforge.com/forums/sho...1&postcount=13
for an explanation of how/why jailkit works like that)
Furthermore, you claim you and 3 programmers are "fixing it" - what is the problem, and how are you fixing it?