Why Linux doesn't get booted automatically only If I changed the BOOT.bin not the zImage, while in the first case it gets automatically booted
The zynq-uboot&gt; prompt is the uBoot command interpreter. root@mcontroller# is a Linux shell prompt. So in the first capture you're up and running in a Linux environment. In the second capture you're still in the bootloader. You'll need to look at the uBoot commands to figure out how to start running the Linux image.