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MSP430F5438A: Running from Flash, Time function does not work

Part Number: MSP430F5438A

Tool/software:

I have created a program that uses 3 SPI and 1 serial interfaces. The program sees the time from debug mode but when I flash it the time is frozen. The time function is part of the TI lib (MSP430F5xx_6xx).  It could be a optimization issue or something else, not sure.  The code does executes for the most part. The SPI and serial interfaces are working and this is not a code crash but the timer is frozen. I am not able to track it down.

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