Sounds like a problem with your .htaccess ...
Are you sure it's not a caching problem on your local side from a previous error you had on the site ?
Can you verify with wget --no-cache
http://domain.tld/ from another computer if it's still downloading the source ?
Because if /administrator is working, your php processing is working, which will prevent apache from giving you the page source ... even if it is the index ... but it is still internally known it's php, because apache is looking for i.e. index.html and index.php and when it finds one of this files, it interprets them when needed - and sends the result back....
So try a different browser, empty your caches first, try wget ... if the problem still exists, turn on apache debugging ... show us the log please.