Hi,
If you have a Due and want to use the stem MEGA or Base shield v 1.2 you may have to hack it so it will work. There seems to be a problem with compatibility with the Due reset that stops program downloads from the Programming and Native USB ports when its in place. Simply remove the reset LED from the board and things seem to work fine. Its easy to twist off with a small needle nose plier. The reset button will still work … at least it did for me 
.