I am currently having the exact same problems, with Vivado 2020.2, running on a LINUX (like Mohammadhgh) and the ZYBO Z7. I don't remember such thing with 2020.2 on Windows (going to give it a try). No such problem with an other Digilent board like the Cora Z7.
The facts with the Zybo Z7 :
- I have the board files properly installed,
- the checkbox "Apply Board preset" is well checked when doing automation,
- when configuring the Zynq IP, everything is empty (No UART, NO GPIOs etc...), hence it synthesizes with warnings and doesn't work afterwards with Vitis (mem crashes...)
It seems something could be wrong with Vivado 2020.2 Linux (https://forums.xilinx.com/t5/Embedded-Development-Tools/Zybo-7Z-HelloWorld-fails-to-execute-consistently-Vivado-Vitis/m-p/1242056) but I think something may be wrong too (or incompatible), with the board definitions of the Zybo, because this does not happen with the Cora Z7.
Thanks,
Vincent.