similar problems happen with Xilinx debugger tools also

There are specific delays and order of commands that may cause the ARM DAP to behave badly, I have had similar issues this also many many times.
When I did the openOCD testing, then it worked, but it was done on windows host. After that work we have not tried with openOCD any more.
Try to let the zynq to boot from some empty dummy FSBL, that may solve the issue