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PWM Code not running correctly after reset

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I have code on the F28M35x outputting basic PWM waveforms. However, when I stop debugging and power cycle the board, the output is no longer correct. I then get a few pulses spread out much further in time, as if the PWM switching frequency were reduced significantly.

I believe I did not have this problem previously. However, I have not changed anything that I think would cause this issue. My code is linked to flash memory:

   .cinit              : > FLASHA      PAGE = 0
   .pinit              : > FLASHA,     PAGE = 0
   .text               : > FLASHA      PAGE = 0

On the Debug Configuration screen, under the Target tab, there is an Auto Run and Launch Options settings page. I have tried checking "On a reset" under "Auto Run Options", but then the debugger does not load code onto the board.

So the question is: Why might my code be running incorrectly out of a reset when it runs correctly out of the debugger?


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