I am currently experiencing the exactly the same issue with the LPC1549 RTC. I have several boards and each of them has got the problem:
Identification: ZSD14372A (Production Year 2014 / Week 37 - Silicon revision A)
I am using a 32 KHz cylindrical Xtal with 22 pf capacitors.
Supply: all supplies are clean 3.3 V
The RTC oscillator frequency is routed to an I/O port thanks to the CLKOUT feature.
My frequency meter indicates 32767,84 Hz - This is a -6 ppm error, yielding a -4 seconds error per WEEK
The counter is used in basic SECONDS mode, without interrupt. I read its value once per second and I send it to my console. After a while, I see the RTC clock going forward several seconds per hour.
Errata sheet LPC15XX 2.2 - 17 february 2017 says:
3.5 RTC.1: Real Time Clock (RTC) does not work reliably.
Introduction: The RTC is a set of counters for measuring time when system power is on, and optionally when it is off. The RTC is clocked by a separate 32 kHz oscillator that produces a 1 Hz internal time reference.
Problem: The RTC COUNT should increment by one in one second. With the problem, the RTC COUNT might increment by more than one within one second, causing inaccurate time counting.
1 - Assuming there is no direct work-around for this issue - Is there a known, simple and reliable way to use the on board 12 MHz Xtal oscillator to achieve coherence checking and remove the redundant pulses whenever they appear ?
2 - has this issue been fixed in new silicon. Are these new devices available ?