I am performing an upgrade for a customer and ran into a weird issue. I've already done a few of these upgrades without issue so I'm lost on what went wrong. Here's the story:
Client asks me to upgrade his MT install. No problem. I download the new version, unpack it, and copy the files to the user's "blog" directory. I run mt.cgi and it performs the upgrade as usual with no explicit error messages.
I login to the user's MT install and the dashboard says it is version 4.1 but when I run Tools -> System Information it says the version is 4.01. Everything looks like it was upgraded properly, the blog runs as intended. However, it is missing the new features of MT 4.1. For example, when I try to create a new blog, it displays the screen from 4.01 WITHOUT the "Template Set" drop down and it uses the old style from 4.01.
I've triple-checked that all of the files were properly replaced. I copied the files using:
cp -r source dest
and the files reflect their new timestamp. Proper permissions on all executables (chmod 755 *.cgi), proper ownership on all files.
I've run out of ideas so I'm throwing this out to you guys to see if anyone has had any similar issues and (hopefully) a solution. Let me know if you need any more information to help diagnose the problem.

Not sure if you know this but this is NOT the support forum for Movable Type in general. It's for "Community Solution" which it seems is needlessly new jargon for forum/BBS software. You'd be better of looking for your answer on forums.sixapart.com, which are the same old Invision Boards.
Hi Brian.... even with the steps you've described, this really does sound like the new files hadn't copied into the right place. The Tools > System Info is kind of the definitive listing of what version the system thinks it's on, and if it says 4.01, than that's the real deal.
Have you tried a clean MT install alongside the old one, instead of overwriting? That would be my best first suggestion.