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Why does our project (CCS 5.4, F28069) now have its PLL go into limp mode?

Our project has been fully functional for some time (the code has not changed in two weeks), but running from RAM.

In the process of tweaking .cmd files to use the FLASH, our project fails the PLL test in InitPll() (SysCtrlRegs.PLLSTS.bit.MCLKSTS != 0) and goes into limp mode, even when we use our old .cmd file.

To make matters more strange, if we run the Example project (Example_2806xEPwmTimerInt) on our hardware, there is no problem with the PLL test.

What is in our configuration that could have changed or gotten corrupted that is causing this problem? I have looked at sprufb0d, but nothing jumps out at me.

Thanks -- Mark