I don't know what to say there, ive never had any issues with my prestige run 

if you say you are logging in a couple times a day it should be working...

Plarium support can get someone to look into your account, your logs are saved 

on the server... so email plarium, and ask them to look in this, if what you said is true im sure they will fix it 

https://support.plarium.com/enpirates/Tickets/Submit/Step1/53

dragonbear3rd said:

Why is it so hard to keep a running tally of loyalty points? 

You need to find out the exact time the day changes for you. On the East Coast of the US, it is 19:00 EST or 00:00 UTC. I use a browser refresh if I am in the game, other wise, I simply enter the game. No need to "login" per say.

I see the new day flashy and click it.

I try to do it as soon as the day flips or as soon after as possible. Depending on where one lives, that could be impossible. Simply playing the game two times in YOUR day may not be close to Pl's day which, for me, flips over at 00:00 UTC as I mentioned.

Another sure way to catch each day is to enter it, with a fresh browser, at the same time every day.

It is rare but possible that using a browser that has not it's cache cleared for months could also affect the game as with a PC battery that is very weak or dead. These two are rare to very rare but possible with the clogged up cache being more possible than the battery.