
Originally Posted by
Hiero Glyph
It's directly related to the EGO spam when you load. The game recognizes you as EGO X (the first EGO rank listed), before it recognizes you as EGO Y (your current EGO rating). As such, if the difference between these two EGO ranks causes you to not have your final slot, it will be removed. So, for example, if you are EGO 3,XXX currently but the first EGO listed says 2,XXX then you will lose your EGO 3,000 perk slot. Sadly, this issue was fixed once already but that person was probably fired so now they have no idea how to fix it a second time.
EDIT: Apparently, the first EGO rank listed can cause you to lose multiple perk slots, not just the final one. Please note that this will only affect your active loadout when you incur the EGO spam on a load.