> i have noticed that there are some sites that have 
an 
> index.html and they cannot seem to be mirrored, all 
> you get is the index.html and a load of empty 
folders 
> if those folders have an index.html within them.

I don't think so - but this might be because other 
links are located in other domains - for example 
www.foo.com/index.html will point to 
bar.foo.com/index.html

Ensure that you defined proper filters and parameters -
 do not hesitate to send me through email the website 
URL if this problem still occur