Mark is correct, On each read of the CNR, software must first write to the CNR with any value.
You can find the description in "42.4.5 LPTMR counter" of K10P144M120SF3RM.

I also notice that you have enable the Timer Free-Running Counter.
When 1kHz LPO is select as clock source. You may need to wait 65536ms , then run into LPTMR interrupt.
![LPTMRx_CSR[TFC].png LPTMRx_CSR[TFC].png](/t5/image/serverpage/image-id/35941iAB459CDA011968ED/image-size/large?v=v2&px=999)
Best Regards,
Robin
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