[eluser]boltsabre[/eluser]
Hmmmmm... I cannot see it being a problem.
Can you remember if you (or anyone else) hacked your core files? I did an update 4 months ago and it took me all day because when I very first started with CI two years ago I changed one or 2 lines of code in one of the core files. Bam... update fail because I replaced my "hacked" file with the new "clean" file, thus breaking my application.
Or perhaps make a copy of your "old" site and try running the update the way they say and see if that makes a difference?