As the majority of users have no such problem I may assume that it is neither firmware nor custom rom related. First possible reason for me: The router, so I may suggest to think about updating or simply restarting or reset it.
As a Networking and Telecom expert, troubleshooting is the first thing i do. However, wrong protocol programming (or implementation) can lead to disasters, S2 used to suck the battery off in 20 minutes from the WiFi DTIM values, so i wouldnt be surprised if Sammy effed up here, but most of the AP's i am around are pretty robust. I personally design WiFi for stadiums and enterprise level deployment, and know WiFi all around, even if AP's are triggering the amnesia, the problem is at the phone,
i personally am not aware that an AP can trigger a passkey database wipe
The reason why i ask is because i help a lot of friends upgrading. 3 of my n7100 mates have the WiFi amnesia, while i have seen Note 3 users posting a lot of this issue, i havent seen much of that on the Note 2 forums, but i myself (Note 3) have the issue, which started with KitKat for both devices.
May i be the problem through flashing? maybe, but i am an advanced user and i know the easiness of Odin, nevertheless, issues are still there even after a reflash/reset.
PS, lately a few S4 phones have shown the same problem, also again after upgrading to KitKat.
Here, just for the reference:
Losing wifi passwords
a few friends noticed that it has something to do while switching to Data connection, but the trigger is really hard to catch. And all of them have different usage, one of them prefers CWM, the other prefers stock recovery, while another one prefers stock with root, so this is definitely not an error made from the user, but rather from the manufacturer
Anyway guys, sorry for dropping this here, i just regularly check to see if i can get rid this annoying issue, yet am surprised to see no moaning about it