Are there any known problems with the RTC using a mainline kernel? I'm currently at 4.9.94 and seeing inconsistant readings from the rtc. I sprinkled twl_rtc_read_time() with some logging and noticed about half the time I get incorrect values.
Also, I noticed (via another thread) you are close to release a 4.9 kernel. Are there patches on your end that are not in mainline that would be avalible?