Hi,
It is very likely that the LPTMR isr you have created does not clear the LPTMR flag. A good way to check this is in run mode. Once the flag crearing is working then you can re-enable the LLS mode entry.
For a complete guide to the low power modes please see an application note I've written on this subject. AN4503.
There are a number of other things to consider. One is the clearing of the LPTMR flag sequence and code execution timing.
The clearing of the LPTMR flag takes a number of cycles (up to 7 bus cycles). If you clear the LPTRM flag with a write to an LPTRM register then you should do a read of the LPTMR register to make sure the flag is cleared before exiting the isr.
This is what I put in my LLWU isr.
if (LLWU_F3 & LLWU_F3_MWUF0_MASK) {
printf("****WUF3_MWUF0 IF LPTMR *****\r\n");
SIM_SCGC5 |= SIM_SCGC5_LPTMR_MASK;
LPTMR0_CSR = ( LPTMR_CSR_TEN_MASK | LPTMR_CSR_TIE_MASK | LPTMR_CSR_TCF_MASK );
LPTMR0_CSR |= LPTMR_CSR_TCF_MASK; // write 1 to TCF to clear the LPT timer compare flag
}
If you do this the LPTMR isr will not be taken and both the LPTRM flag and the LLWU flag are cleared. Writing only to the LLWU module llag is not required and will not clear the LPTRM flag.
I hope this helps,
Philip