Follow-up Comment #1, bug #20426 (project mypaint):
MyPaint doesn't modify Xorg settings.
It may be possible that GTK+ does it, but I doubt it. I guess there is a bug
somewhere else, in Xorg or in the wacom drivers.
Also, MyPaint will paint before the "click threshold" is reached (I assume
that's the threshold you mean), thus this threshold setting is of no interest
at all, as far as MyPaint is concerned.
I think you have to search this bug elsewhere...
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