Dear Babar,
I am sure that you must have read my coments regarding your problem.
I think one off the 24bit counter ls7166 might be the reason for your problem.
If you can do the parts desolderning, then remove all the eight counter ic
and install them one by one in the 20 pin turned pin ic socket.
Use the related counter postion.
This will help you to screen out any faulty counter ic.
Nasir Ahmed.