This seems to be platform independet (PC, PS, XBOX)
It still happens on stable 1.16. I am using a Playstation server on nitrado and provided detailed reports at https://forum.nitrado.net/thread/19762-whitelisted-players-kicked-out-of-server-with-not-whitelisted-error-when-game-se/
It seems whitelist.txt is at time read when the file is "locked", thus it reads an empty file (or fails to read). DayZ server detects it, and repeats the loading of the whitelist.txt right after.
However, this is enough to kick out all players.

This is an example of the RPT log entrie:

19:36:46.757 Reloading Userlist ban.txt
19:36:46.757 Reloading Userlist whitelist.txt
19:36:46.757 Player <hidden1> (<hidden1>) kicked from server: 12 (You are not whitelisted on this server.)
19:36:46.757 Player <hidden2> (<hidden2>) kicked from server: 12 (You are not whitelisted on this server.)
19:36:46.757 [Disconnect]: Client <hidden1> early disconnect
19:36:46.757 [Disconnect]: Client <hidden2> early disconnect
19:36:46.773 Reloading Userlist whitelist.txt
19:36:46.773 [Disconnect]: Start script disconnect <hidden1> (dbCharacterId 1 dbPlayerId 1) logoutTime 5
19:36:46.773 [Disconnect]: Start script disconnect <hidden2> (dbCharacterId 31 dbPlayerId 31) logoutTime 5