I installed Mint 13 through Windows,
You have performed a Mint4win installation.
but it does not keep changes/updates when I reboot (same as using live CD).
You are experiencing the same problem which has been reported and solved in this thread e.g.: New Settings Not Persistent Between Boots
You will not experience the same problem when installing Ubuntu via Wubi, because Wubi manages to perform phase 2 of the Wubi installation automatically, whereas with Mint4win you have to click on "Install Linux Mint" manually. (The details can be found in the thread to which I pointed above.)