Dear @ctgraham
The problem with conf-files and .htaccess seemed to be related to the !-d command. Here is an output from the logging:
RewriteCond: input='/' pattern='!/index.php/' => matched
RewriteCond: input='/var/www/html//' pattern='!-d' => not-matched
I now removed the !-d commands and instead used the command as described elsewhere by @ajnyga How to remove index.php in ojs 3.0.2.0 - #15 by ajnyga :
RewriteRule ^(folder1|test)($|/) - [L]
However the main problem still remains.
But this work-around makes it work:
I use Apache/2.4.6 with CentOS.
The best,
Edvin