If the file contains UTF-8 encoded characters or plain text then its treated as UTF-8.
If the file is found to contain extended characters that are not valid UTF-8 then its loaded as ANSI.
It has to be done this way, otherwise we experience the problems you first discovered.
If you load a file that is detected as UTF-8 but want to save it as ANSI you can do this under File > Save As, then on the Save As dialog change the Encoding to ANSI/ASCII
In most cases you'll want to save as UTF-8 (if the file is detected as such)
Alternatively you can use an external editor with FlashFXP such as
notepad++