User settings should be okay at second run. (That's a bug in the launcher.)
However, the reason why stuff doesn't work is that the server the launcher is trying to connect to to check if the client is ok isn't responding. Since the repair tool is using the same server, for some the repair tool doesn't work either. For those who patched before the content server became overloaded everything went well - including Chribba, who offers a copy of the updated files
here or
torrent here. It should be possible to just copy those files over the client files and get things working by launching directly to the client via "exefile.exe" in the "bin" folder inside the EVE installation folder (default C:\Program Files\CCP\EVE). Naturally, since those are third-party supplied files, practice caution.
Chribba himself posted those links, haven't noticed any Veldspar pr0n to seep on my computer yet.