The line cycle accumulation procedure seems to be fine. But I have another question. What is the value set to in ZXSEL bits of the LCYCMODE register? This selects the phase voltage whose zero crossings are considered for line cycle measurements. That might need to be adjusted to point to just one phase voltage, and make sure that the particular phase voltage is more than 10% FS in amplitude level. You must get an LENERGY interrupt after 5 secs based on your LINECYC register setting ( for 50 Hz input). If not check to see if there is a SAG detection in that corresponding phase or a ZX missing interrupt.
Regarding your other question about negative PF and powers, can you provide a set of example data that you have collected which show erroneous results. State your input conditions as well. That might help me to understand where the error occurs.
Regards
hmani