Hi @MCW ,
Thanks a lot for your cooperation for the new question post.
Now, please let me know your used platform and chip at first.
Normally, the auto probe should not influence the flashing.
I think you need to check these points:
1. Do you connect the auto probe to the JLINK JTAG interface or not?
2. Which board you are using, NXP EVK?
3. Which external flash you are using?
4. Can you reproduce the issues with the NXP EVK board? Segger JLINK or the on board JLINK firmware?
If it is the customer board, please also share your JTAG interface connection situation.
5. Which JLINK firmware you are using? JLINK driver default flashloader?
Please help to confirm the above questions, then I can help you do the detail checking.
It's better to reproduce the issues on the NXP EVK board, if not, it may related to your custom board.
Best Regards,
Kerry