Why does OS X 10.9 forget system preferences?

I'm new to Macs, having just transferred over from Windows, so please bear with me if I appear to be asking something very obvious.
Anyway, I'm running OS X 10.9.4 on an Mac 21" 2.7 GHz, and have set up a few preferences in the System (such as mouse gestures, automatic hiding of the dock etc.) But, every time I shut down, the system appears to have forgotten my settings when I boot up. It doesn't take long to re-set them, but it's a nuisance.
Is this a known problem? Is there a solution?
All help gratefully received ............

In fact I've realised that there a number of things that the Mac isn't remembering to do:
1) it isn't remembering the system preferences I select (as above)
2) I installed an extension for Safari, the DuckDuckGo search tool. Each time I open Safari, it asks me to go to the Preferences>Extensions window and either enable it or uninstall it. Whichever I do, the computer isn't remembering the selection when I quit Safari and/or shut down, and the next time I open Safari, I have to go through the same routine.
3) For some reason whenever I log in, it opens the Mail program, even though it isn't listed as a login item in System Preferences>Users, and my default mail program is Outlook (in fact I've never knowinglyl opened Mail). When I want to shut down or restart, I always quit Mail. The appropriate command from the Apple menu gives me the option of reopening windows when I next log in. I always choose not to reopen windows (thinking that that way it will prevent Mail from reopening) but when I reboot, there it is.
As I say, this is all very odd as an identical Mac bought at the same time hasn't got any of these issues.
Am I being very silly and missing something obvious or is there a problem here?

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