in case you are using the synaptics driver (
http://freshmeat.net/projects/synaptics/)
there is a program to configure this driver 'synclient'
when running it will show the config the interesting one are:
VertTwoFingerScroll = 0 (by default 1)
HorizTwoFingerScroll = 0
so run it as :
'synclient VertTwoFingerScroll=0'
probably this is more the behavior you like.
you can use 'man synclient' to see more options to configure because this driver supports
more things which might be useful