Hi
I use sam-ba on Ubuntu 12.04 with Eclipse. I wrote a makefile wherein Sam-ba is run using the command line. I found a bug when I want loaded binary in flash. The problem comes from locks bits of memory. When you use gui, sam-ba asks you if you want to unlock these bits. If you answer "yes", a variable is set to 1. In command line mode, this variable is not set and therefore it doesn't work!
You can solve this problem by adding "else {set ForceUnlockBeforeWrite 1}" at line 2168 of file tcl_lib/common/generic.tcl.
I hope that it can help someone...