That has not happened to me (above). My preference setting for double-click speed stayed in place. It should not change.
So why? -- Perhaps a conflict with something else and I think of my use of BTT (the freebie preference software I've previously mentioned). It also has speed and sensitivity setting. -- so I had to set my settings in both these preference.
Maybe worthwhile messing around with BTT, since it does also has seed and sensitivity settings for the trackpad, even if you're not interested in it's other features.
!? - I don't know or have any connection with BTT, by the way; but it's free so I tried it. There are also OTHER people who make software to help control the trackpad (jltouch -
http://www.jitouch.com/index.php?page=jitouch ) -- is $6 but they indicated they were working on a new version update to now include this new Magic Trackpad, so I didn't try them.
But_ Preferences are not suppose to 'just change,' for no reason at all. The 'old computer trick,' comes to mind: delete the preference pane and download the software again and reinstall.