I've done in_mouse 1 and in_restart and it didn't fix it. However, if I change my sensitivity to 2the mouse works fine. But it's way too fast.
My mouse settings are:
//{{{ mouse sensitivity
seta sensitivity ".60"
seta cl_mouseAccel "0"
seta in_dgamouse "1"
seta in_mouse "1"
seta m_filter "0"
seta m_pitch "0.022"
seta m_yaw "0.022"
//}}}
The mouse is a Razer Copperhead with the evdev driver.