Does the Microsoft Intellipoint software work with Mountain Lion?
I believe I have discovered the real reason why this happens and the cleanest work around (version 8.2 doesn't fix this for me).

Why this happens:

The issue for me was tracking speed (and mouse acceleration!) reverting to the OS X default and not using Intellipoint settings. After trying to learn AppleScript for 2 hours to hack around the issue and adjust my sensitivity settings through an automated script to adjust the preference pane, I remembered there should be a process called 'MicrosoftMouseHelper' loaded for the Intellipoint to work, and I noticed it wasn't running on a clean reboot. This, I believe, is the issue as it must be run to activate the hardware and software features for the mouse. (Use Activity Monitor to check yourself if this is running on clean boot and it likely won't be running, or if you already opened the preference pane as per @tquang's suggestion, kill MicrosoftMouseHelper process and see the mouse behaviour change). When you open the Microsoft Mouse preference pane, the above process starts and stays in memory after you close the system preferences, hence why you only need to open the preferences then close, and why @tquang's approach works rough-enough.

Heres my cleaner/less-intrusive solution:


Open Finder.
Navigate to: /Library/PreferencePanes/.
Right click on "Microsoft Mouse.prefpane".
Select Show Contents.
Navigate through Contents > Resources.
Leave the above open, and now open System Preferences.
Select Users &amp; Groups.
Click on your user, and click Login Items.
Go back to your Finder window, select the file "MicrosoftMouseHelper", and drag this into the login items area on the right-hand side of the login items page (in the System Preferences window).
Intellipoint settings should now be loaded at login, overriding the default OS X settings for pointer speed, scrolling, and buttons.