Hello Per-Siden,
I guess I have a more or less good workaround.
Uncheck Autodetect character encoding from Settings->Preferences->MISC.
In Settings->Preferences->New Document select the Encoding you want by using the dropdown list.
If you use the session functionality Settings->Preferences->Backup take care that you close
any document with different encoding before restarting npp, otherwise it will load the codepage
from the information within then session files.
Cheers
Claudia