When now feature of mousetweaks is enabled, the mousetweaks process
normally does not run; so it should not be responsible for the problems
that you see.

Considering your remark about gksu, I wonder whether at-spi is not the
root of the problem. In fact, at-spi is known to be incompatible to gksu
and the incompatiblity shows up when there is a program actively using
at-spi. (This might explain why mousetweaks seems the culprit.)

Since version 2.31.3, mousetweaks does not need at-spi anymore. In
lucid, you can install a version that does not need at-spi from the
following PPA:
https://launchpad.net/~frafu/+archive/ppa?field.series_filter=lucid

If you do not need at-spi for something else, you could try disabling
at-spi and use mousetweaks from the PPA indicated here above.

Please, let us know if the problem continues to occur when at-spi is
disabled.

-- 
mousetweaks went to 100% cpu load and X system is frozen
https://bugs.launchpad.net/bugs/384754
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