How to I fix software center after installing the Linux Mint MATE desktop?

I had the same problem with Software Center and some other apps. However, you don't need to do a reinstall though that's probably advice too late. Here's why it doesn't work:

lsb_release -a

prints:

Distributor ID: LinuxMint
Description: Linux Mint 12 Fluxbox
Release: 12
Codename: lisa

and that can be corrected to keep Mint-Mate by doing this:

gksu gedit /etc/*release

and change everything in the file gedit brings up to:

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=11.10
DISTRIB_CODENAME=Oneric
DISTRIB_DESCRIPTION="Ubuntu 11.10"

Then run:

gksu gedit /etc/*issue

and change to:

Ubuntu 11.10 \n \l

Worked great for me though Mate seems a bit rough around the edges but as I am purely testing Oneric in VBox it's no matter

_{converted my comment to an answer}

This upgrade process is similar to the use of the Gnome 3 PPA in Natty.

The upgrade involves upgrades to 300Mb+ of software libraries - it is really a one way process.

You could possible install over the top of your existing installation (and hence retain you existing /home folders) - but you'll need to reinstall all other applications.

Backup first though using something like clonezilla/partimage.

I tried resetting lsb-release and *issue, but for some reason, they always revert to linux mint. I'm not sure if they reset on each restart, or on each update, but they do reset frequently.

I wrote a small script which I manually run every now and then:

#!/bin/sh

echo "Restoring /etc/lsb-release ..." && \
echo "DISTRIB_ID=Ubuntu" > /etc/lsb-release && \
echo "DISTRIB_RELEASE=11.10" >> /etc/lsb-release && \
echo "DISTRIB_CODENAME=oneiric" >> /etc/lsb-release && \
echo "DISTRIB_DESCRIPTION=Ubuntu 11.10" >> /etc/lsb-release && \
echo "Restoring /etc/*issue ..." && \
echo "Ubuntu 11.10 \\n \\l" > /etc/*issue && \
echo "Done."

Save as (for example) fixubuntu.sh and set execution permissions on it (chmod 755 fixubuntu.sh), and execute as root (sudo ./fixrelease.sh) every time you want to restore your ubuntu release information.

Of course, you might want to run the script automatically at every boot. Just make sure it is run as root.