Hi kicad1978,
Sorry for my later reply.
Yes, I know you don't want to modify the hardware and the software.
But in the design phase, we need to find the root problem.
Now, two ways to test it:
1. Find a official board, take an example, FRDM-KL27, you can download your code to the FRDM board, then check, whether it will also turn back to bootloader mode.
If the FRDM-kl27 also have the problem, we should check the software.
2. Try to add the external 4.7K to 10k external pull up resistor on your own designed board.
Then check whether it have the problem.
Actually, if you check our kinetis L Peripheral Module Quick Reference.pdf, page 23, you can find this description:

So, you can try it on your side at first.
Any updated information, just kindly let me know!
Have a great day,
Kerry
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