The RTC Time Seconds Register (TSR) and Timer Prescaler Register (TPR) do not increment while the K65 is running/single stepping (nor powered off with a battery connected).
The tower does not have this problem. Both TSR and TPR run (constantly increment) and when powered off/on the TSR is updated to reflect the elapsed time.
Furthermore, the KSDK example rtc_example_twrk65f180m sets an RTC alarm and waits for it to happen. This works on the tower and not on our board.
I'm thinking there is some K65 errata that Freescale/NXP don't know about yet.
Could this be related to MCG clock speed?
Has anybody seen this problem or does anyone have any idea how to fix it?