I corrected this by using external pull-ups of about 2kOhm from the input pins to pin 14 (output Autofeed), which gets initialized as HIGH. (This is a hack. Better would be using +5V from e.g. the PS/2 connector, but this means another connector, which is too much trouble)
Try this hack, if you've got the same problems.
#include <OpenTracker/tool/disable4786.h>
#include <OpenTracker/input/ParButtonSource.h>
#include <OpenTracker/input/ParButtonModule.h>
#include <OpenTracker/tool/OT_ACE_Log.h>
#include <iostream>
#include <sys/ioctl.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
Include dependency graph for ParButtonModule.cxx:

1.4.6