Wim Cosse

I have exactly the same problem but with me it was with a new website.
only the main page is visible and with the permalinks other than default the other page’s will not be found error 404 or redirect loop
checked with a older installation wordpress 3.8 and there was no problem so it must be 3.9.1

oh yes and i have a .htacces
running centos 6.5 with wordpress 3.9.1

some times If you go to /wp-register.php or /wp-signup.php it reveals the custom login url…

then you can login with your credentials .