1. I configured and installed cnee with:
  ./configure --enable-xinput2 --enable-verbose -enable-buffer_verbose --prefix=$HOME/usr
  make
  make install

2. I recorded mouse movements in center of first screen using:
  ./cnee --record --events-to-record 1000 --mouse --keyboard -o cnee_test.xns -e xnee.log -v

And I tried to reply them with:
  ./cnee --replay -f cnee_test.xns -v -e xnee.log -ns


But when replaying events, pointer moved to (0,0) corner on the second screen (that's on left side of first screen), and didn't move anywhere else.

Next, I tried cnee with disabled xinput2:
  ./configure --disable-xinput2 --enable-verbose -enable-buffer_verbose --prefix=$HOME/usr

and this time it worked, with minor bug: http://savannah.gnu.org/bugs/index.php?39207

I think this bug is related with bug described in this mail:
http://lists.x.org/archives/xorg/2008-November/040828.html

I tried program from that mail (slightly modified so it compiles with modern X11 which doesn't have XQueryInputVersion function - there's XGetExtensionVersion which can be used instead), and
XTestFakeDeviceMotionEvent seems to be always moving cursor to (0,0) coordinates - except when it gets relative coordinates.

I don't know if it's really xnee bug, but maybe there is some workaround.

Tested with:
X Server version:
X.Org X Server 1.13.4
Release Date: 2013-04-17


Extensions:
XTEST 2.2
XInputExtension 2.2
RECORD 1.13