Yesterday I used the mutouch-Xorg-driver under debian etch (Xorg 7.1), worked without problems. Then I upgraded to debian lenny (which has a newer Xorg server, 7.3) and had the problem that the y-axis was inverted; so if I touched at the top, the mouse was at the bottom. There's no option for the driver to solve this with config-options (at least i could not find any), so I took the code and changed one line, now it's working.
It's line 746 in xf86MuTouch.c I changed from
cur_y = WORD_ASSEMBLY(start_ptr, start_ptr);
cur_y = (priv->max_y + priv->min_y) - WORD_ASSEMBLY(start_ptr, start_ptr);
That inverted the y-axis for me, now everything is working again.
Maybe someone can take a look at it if this change is ok and maybe commit the change to the mutouch driver so hopefully the bug disappears.
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this seems to be fixed in git, but not in any release yet. I'll try to
get the patch in lenny soon, so you can confirm that it's fixed.