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I like to swap my mouse buttons (like a left-handed person) and use a slightly faster pointer speed than the default.

Why on Windows Vista Home Premium do I have to restore these settings again and again each time I reboot? Is there any way to make it permanent?

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UPDATE: I did not find any option in setpoint to change the settings of buttons 1 and 2. For now I've worked around the problem by getting into the habit of 'Sleeping' the computer instead of shutting it down and rebooting every day. – Alex R Nov 14 '09 at 18:05

Are you using a Logitech mouse? It seems it installs a program that resets these settings at startup - a violent crime.
Even after uninstalling the drivers, the program remains. This forum post suggest you should remove a program called Setpoint.exe from startup, using msconfig.exe (type msconfig to the start menu run box, and uncheck Setpoint.exe)

Edit: Phoshi comments, quite correctly, that you can simply use SetPoint to configure your mouse.

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Don't uninstall setpoint! It's really not that bad, and does add a fair amount of functionality to the mice. Just configure it in setpoint :P – Phoshi Oct 31 '09 at 10:45
Thanks. But setpoint doesn't give the option to configure the two primary/secondary buttons, only all the other buttons. Unless I'm missing something... how do you swap buttons in the setpoint settings utility? – Alex R Oct 31 '09 at 15:24
UberOptions allows this. – Phoshi Nov 23 '09 at 15:56
up vote 0 down vote accepted

The problem actually appears to have fixed itself. I suppose there must have been an automatic update that took care of it.

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