If you have done no changes to the motion.init file then the problem is more than likely the sensor for the capper tray. there are a couple of sensors for the capper. one inside the carriage , left side near heads that is suppose to look for the capper tray when it gets push up into the bottom of the carriage. It could be blocked or fouled with ink or just out of align.
The other is behind the from left access door in the same cabinet as your waste tank etc. look up at the top of the cabinet it should have a yellow sensor. More than likely it the carriage sensor.
What else is wrong.