I had the same problem and it turned out to be a combination of several things.
I had to disable the BDM bit in SOPT1 and run the circuit with the BDM disconnected.
I had a floating input and an output trying to pullup a load.
I also had to do the following:
ldhx #SPMSC1
lda 0,x
and #%11110111 ;clr LVDSE bit
sta 0,x
bclr ICSC1_IREFSTEN,ICSC1 ;disable clk in stop mode
Disable the low voltage sense and disable the internal clock.
In my case, I was still drawing approx 70 uA... which was not acceptable. It turned out that I was using the internal IRQ pin pullup and had a 1Hz square wave waking up the processor every second via the IRQ pin..... I disabled the internal pullup and used an external 470K pullup instead. The circuit works great and power consumption of approx 3 uA that includes also powering the RTC, a couple other ICs.
Hope this helps you or anyone else out... That took a couple days of scratching my head to resolve.
Paul