Hello to you,
I have investigated your case and seems it is a ~10% drift from the base time this is because the maxim tolerance of the LPO clock is +/- 8% and another reason is that the using of LPO acordingly to Reference manually
" Alternatively, the time counter can be clocked by a LPO 1 kHz clock and the prescaler will increment by 32 for each LPO clock"
so the base clock for 1second is 32768 Hz, with LPO is 32000 Hz this is an increase of 2.3%.
To do the compensation you need to have a reference clock from wich to calculate the deviation for compensation !
The best aproch is to use a external RTC cristal or TCXO with 32,768 Khz if you want to have no deviation !