I have been playing around with a SAMA5D2 Xplained board.
It seems that if EDBG is re-programmed as Jlink, code disassembly is treated as *big* endian by mistake when using JTAG. This results in 'garbage' instructions.
SWD works fine (little endian instructions)
Also when using JTAG I have noticed writing to memory via JTAG is not reliable (sometimes top bit is not set). SWD looks OK.
P