I've had this issue as well for a while. I've been overriding gnome-
control-center with 'xset m default'.

Mouse speed is normal at gdm. When I log in, it immediately goes to a
crawl. 'xset q | grep accel' reports acceleration: 3/10 threshold: 0.

If I remove .gconf/desktop/gnome/peripherals/mouse/%gconf.xml and log
out, the problem does not re-occur on next log in until I open the mouse
applet again. When I first open the mouse applet the slider is in the
middle. If I move it, it goes to the left and my mouse speed is back to
3/10. When running gnome-control-panel in the foreground of a shell, the
mouse applet reports:

(gnome-mouse-properties:8550): capplet-common-WARNING **: Unable to find a 
default value for key for /desktop/gnome/peripherals/mouse/motion_acceleration.
I'll assume it is an integer, but that may break things.
Please be sure that the associated schema is installed

(gnome-mouse-properties:8550): GConf-CRITICAL **: gconf_value_free:
assertion `value != NULL' failed

(gnome-mouse-properties:8550): GConf-CRITICAL **: gconf_value_get_float:
assertion `value->type == GCONF_VALUE_FLOAT' failed

After modification of the acceleration slider,
.gconf/desktop/gnome/peripherals/mouse/%gconf.xml contains the following
line (among others):

        <entry name="motion_acceleration" mtime="1181840944"
type="float" value="0.20000000298023224">

Note that 'xset q | grep accel' returns acceleration: 2/1 and threshold:
4 after 'xset m default'

It may be worth noting that I have a similar problem with keyboard
autorepeat.

-- 
mouse preferences acceleration not saving
https://bugs.launchpad.net/bugs/118593
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