I can confirm that I experienced this (on Xperia 10ii dual sim following flash of 4.1.0) where my Wifi network password was not retained. There were also other situations where, following flashing the OS, initially logins and credentials weren’t saved. After a reboot however this seems to have fixed the issues.
Examples - Google Account sign in not saved. Audio recorder app appeared not to have saved recordings (In fact recordings were saved but were not shown under Recordings tab until after a reboot.)
Also I was initially unable to complete registration of Whisperfish (Reported under Whisperfish thread) until the phone was rebooted since the registration hung after input of the OTP Signal code.
Hope this is helpful in identifying possible cause.