Reported by Alexander Elbs recently on the Debian BTS, he's using 1.9.100 on a MGA G400/G450 (rev 82). See the URL above for the full config and log. He says:

"my two outputs are configured this way:

xrandr --output VGA1 --preferred --right-of VGA2
xrandr --output VGA1 --mode 1280x1024 --rate 75
xrandr --output VGA2 --mode 1280x1024 --rate 75

When I use krdc (rdesktop) to a windows client or nxclient to
another linux box the mouse pointer gets set to the wrong
position when the mouse pointer should be inside that
window.
It seems the mouse pointer is shifted one screen to the right:
When the rdp window is on the left screen and the mouse pointer
inside it I can see the pointer on the right screen. The pointer
behaves normally otherwise e.g. it changes its form at the edge 
of a (remote) window, but its very hard to find that edge of
course :)
As soon as I leave the rdp window the mouse pointer jumps back to
its correct position.

With 'xrandr --output VGA1 --same-as VGA2' I don't get this behaviour:
everything works fine."