What are you doing when inserting a pen that requires you to lower it?
(We have occasionally seen people insert a pen in the “pen down” position, and then manually change the pen-down setting, but that’s the opposite of the recommended procedure.)
The EBB firmware is open source, and hosted in the EggBot repository: https://github.com/evil-mad/EggBot/tree/master/EBB_firmware
The other I/O pins above the servo connector are not polled by default, but you can poll them through software, for example by modding an extension. We would always recommend to use the existing interface rather than modifying the firmware, especially for things like this that are easily done through software: http://evil-mad.github.io/EggBot/ebb.html