I'm struggling probably through the same issue where i've been using SerPro protocol open sourced by Alvaro, it has been working for more than 2 years within different MEGA (1280, 2560 rev 2 and rev 3) on different projects. When It will work OK then download on DUE but the SerPro protocol using Serial standard routines does not work. Please note that SerPro is an implementation HDLC on top of USB protocol plus has object oriented programming to add very easy any RX or TX commands coming from a GUI (Mac, PC or Linux) so among other things, has 16-bit CRC detection.