I've got exactly the same problem. Since using the updater is way too slow, I downloaded the new client, and installed it after having uninstalled the old one. Then I used the updater, as advised above. It updated docs/credits.txt, updaterconfig.xml, pss, psc and failed to update a thing named "up". Maybe that's part of the problem. By the way, I tried a ping on the server through the updater, and it didn't respond (but is this supposed to work?). What should I do now ?
EDIT : It seems that I fixed it. Or that there was no real problem to begin with. The update problem seems to be a Linux-specific one, and has already been adressed, with a way to correct it somehow.