I'm quite sure if the board works properly (U-boot output is visible), than RCW loaded in board flash is correct and you do not need to use jtag file with RCW override. However, if you are using our board and board settings are set as desired, than this RCW override value (jtag file) should also work properly. Please compare RCW value you have programmed in onboard flash with RCW value specified in 8309TWR_HRCW_jtag.txt to understand the difference.
If the issue is not related to RCW (for example if you see the same result when jtag file is not used), and another board works properly in this particular debug setup, than we can consider debugger and debug probe are set correctly, and the problem is with debug interface (JTAG port) on the board.
We have similar problem here in lab with SOM board, it works properly but does not respond to JTAG. This is board issue.
Please follow board warranty repair/replacement procedure described in warranty card enclosed in board package.
Have a great day,
Alexander
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