application setup problem with virtual directory

[Microsoft]

Hi,

It seems that the default setup project in .net web application
creating virtual directories in the wrong way, when I check the properties
of these
virtual dirs its not something that I saw before when I create them
manually.
Any reason ?
I am asking because I can no longer export iis configuration to another
as long as these dirs are not configured well.
To be clearer - when I create a VD manually I see in properties "a directory
located on this computer"
when .net create it I see "the designated directory"

Thanks
Danny