Setting breakpoints solving the problem sounds a little wierd. Might be interesting to see the log generated by the SEGGER software. See section 3.10, "SEGGER Troubleshooting", of the MCUXpresso IDE v10.02 User Guide.
Also are you seeing this with a standard off-the-shelf project, or is it something you have pulled together yourself?
Finally, please can you confirm what version of MCUXpresso IDE you are using, and also the version of the SEGGER software (and it might be worth installing the latest from their website too and seeing if that helps).
Regards,
MCUXpresso IDE Support