Continuing the discussion from Mouse wheel emulation broken on thinkpad keyboard:
It turned out that the problem was due to keyd which is a keyboard remapping deamon I run to enhance usability of the keyboard. When disabling keyd scroll wheel emulation worded again.
The solution is to ignore the “mouse part” of the keyboard as follows (id given for the keyboard model I use) in /etc/keyd/default.conf.
[ids]
*
# the following line is the id to ignore, use 'keyd monitor' to learn about ids
-17ef:6009:ab84dcc1
[main]
#leftalt = layer(leftalt)
leftalt+left = pageup
leftalt+right = pagedown
# Maps capslock to escape when pressed and control when held.
capslock = overload(control, esc)