Hi Jois,
We are aware of a boot up issues on the MMPF0100 on revisions Pass1.0 through Pass1.2, typically if power is removed from the board and reapplied within ~ 2 minutes. On MMPF0100 revision Pass2.0 this issue was corrected. For more details, see the PMPF0100 ERRATA, Issue #ER19: http://cache.freescale.com/files/analog/doc/errata/MMPF0100ER.pdf
Just make sure that you have a new revision of the MMPF100 or you would need the workaround mentioned in the errata document.
This boot-up issue can also be related to the POR configuration, try to extend the POR to meet the RTC_XTAL stability as mentioned in this community thread: https://community.nxp.com/thread/382025
I hope this helps.
Have a great day,
Jose
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