I also had this bug, it is fixed upstream in xf86-input-evdev  in commit
bb9b4146cb828bd366675e8736fc145e92c9269a

Until this is fixed in the repositories I've rebuilt the package as
described here: https://help.ubuntu.com/community/UpdatingADeb, using
the patch from here: http://cgit.freedesktop.org/xorg/driver/xf86-input-
evdev/diff/?id=bb9b4146cb828bd366675e8736fc145e92c9269a

This fixes the swapaxes being ignored on my system.
The invertX and invertY still seem to be ignored, but this can be worked around 
by changing the calibration from "0 1024 0 1024" to "1024 0 1024 0"

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which is subscribed to xserver-xorg-input-evdev in Ubuntu.
https://bugs.launchpad.net/bugs/1103723

Title:
  the evdev driver of Xorg ignore the swap axes optiopn for N-trig
  multitouch

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