When I originally installed WordPress on my Ubuntu Linux system I did it via apt-get. This installed the 3.3.1 but disabled all future core updates. So I had to do a manual update. However the files are not in the usual places so I had a bit more work to do.
However it all worked, there was a bit of faffing with directory permissions and ownership, and the site is good. The DB update worked without a hitch which was just as well as I backed up the wrong DB!