Hi David R,
I already find the root problem, it is really very difficult to find it if you don't give us the project.
Your problem is not caused by the chip hardware, also not the code itself, it is caused by the debug configuration in the codewarrior.
You select the KL16Z32M4 not the KL16Z64M4, then the debug will use the 32K to debug your code, after your code larger than 32K, it will have problem.
This picture is from your debug configration: run->debug configuration

Please modify it to MKL1664M4.

After you modify it, then click ok, and debug, your problem will disappear!
Wish it helps you!
If you still have question, please contact me!
Have a great day,
Jingjing
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