I had a similar result. Manually updated all the files in ALL the folders, aside from ones I considered should be kept (about 4 including config, login,psas and settings.
It assured me my Upgrade was successful (and accepted my username/password combination) but didn't take me to the Dashboard and the Blog site was - A BLANK WHITE SCREEN
Further checks in Direct Admin showed my recent logins were to my OWN IP instead of the Blog IP - don't know what caused that or how to fix it.
WHAT I DID:- I noted the four files needed to be changed and did that. When I logged in WP upgraded satisfactorily.
I did notice I still get the "files need cleaning up" message related to the Auto-Upgrade thingy but it reads the 'version' file so I'm happy to see 2.6.3
It seems to me, given answers like (swap the 4 files) could have been made available at the outset, WP go out of their way to unduly complicate this business. JOOMLA was always more sensible, in my opinion and upgraded very simply - but my old Host crashed and I swapped to WP when I restarted the Blog. Always, keeping matters simple is the best - in the event a simple fix is insufficient, there will always be geeks and nerds falling out of trees to give uber complicated solutions.
Besides that, Thanks WordPress for having a Blog Platform that is universally accepted around the Globe and that works very well - when it works. heh
Please try to come up with honest and simple answers in future, like the 4 FILES SOLUTION, in every case where it's possible.
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