The login (index) page for Emilda 1.2 looks for a file called .setup in the Emilda directory. If that file is not writeable by the web server user (usually apache or www-data) Emilda setup cannot update it, therefore prompting to run setup everytime the login page is loaded. To fix this run the following commands in the Emilda directory:
touch .setup chmod 666 .setup
The next time you enter setup, the file should be updated correctly.