On my Kubuntu 10.04 system, my touchpad settings get reverted to the default after a suspend/resume cycle. Ultimately, the investigation revealed that the device itself is disappearing and reappearing. I think either the X server or the input device drivers should detect this and handle it appropriately. I must admit, though, that I am not completely familiar with the situation; it may be that the proper place to fix this is in the Linux kernel or udev. Ubuntu bug report: https://bugs.launchpad.net/ubuntu/+source/xserver-xorg-input-synaptics/+bug/399902
I should also say that I recognize that this problem ultimately stems from bad system firmware, but I am not in a position to change that.
when you suspend, some devices are removed. the server can't differ between a physical removal and a removal caused by the suspend. when the device is added it is added with the default settings or as specified in the config file. The fix for this is to use a tool that persistently sets the values (gnome-mouse-properties does this these days) instead of synclient which only changes the values temporarily. I'm not really keen on putting detection for this into any driver, sorry. It'd cause more pain that it's worth and the time can better be spent improving the GUI tools
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