Don't double up the config file obviously.. Paste over it.. What I find, is sometimes kai doesn't manage to get everything downloaded, then I try again and it usually works.. I think my system ini is older than the one in the link as well, mine only has 4 mirrors..
I do wish the launcher would automatically retry when it fails to load (especially since alot of ppl will be leaving their pc).. I also wish that it counted the time since previous launch to avoid the system download when it just isn't necessary.. Granted I don't understand what the implications of somebody using an outdated engine on the system, but if ppl leave the engine running all day then they must run outdated engines for a short time atleast.. Its just annoying when I reopen the program after a crash and it wants to go through its spiel again..