I had the same problem, and decided to run it into the ground (by doing
grep -r until I found the script changing those files!).
The culprit is
/usr/lib/linuxmint/mintSystem/mint-adjust.py , which is installed by the package mintsystem (on which MATE depends). Apparently it runs at startup, and keeps changing those files to provide Mint-based info.
As you noted, you can recover normal Ubuntu Software Center behavior by putting the correct info in the files:
(Fixing issue.net is not really needed to fix Software Center, but here for completeness. It holds system info that's displayed at the beginning of telnet sessions, and Mint writes its system info there, too).
Conveniently, Ubuntu also writes the correct, current system info in a separate set of matching files which Mint doesn't touch, so you just have to copy them over:
I've given up on MATE since I'm happy with Cinnamon running on Ubuntu 12.04, but one fix would be to just comment out the offending lines in this script (you don't have to be a python geek to figure out which section is the problem!)
A more polished fix would be to use the LinuxMint overwrite system (explained in the file
/etc/linuxmint/adjustments/README ) to manage the corrections - but I imagine that either of these solutions will be borked once the relevant files are updated (or you update Ubuntu base).
The best solution would be to convince the mintsystem package maintainers that Mint is a victim of its own success - now that many people are installing MATE, even on Ubuntu, it shouldn't be calling mintsystem scripts which assume a LinuxMint base install.
But I will leave that battle to someone else. As far as I can tell, Cinnamon doesn't trigger this behavior, so hopefully I won't run into this problem again. :).
EDIT: For those of you who are interested in trying MATE on Ubuntu, these instructions seem to avoid this problem:
How to install MATE on Ubuntu
The mistake I made is going to the Mint repository (rather than the specific MATE repository) and installing a bunch of packages labeled 'mate', eventually pulling in the
mintsystem package, which caused the problem.