baltzis wrote: The problem then occurs because of this structure of my root directory?
Since Limesurvey and Joomla are doing operations on the URL, it is not the recommend to install them inside each other.
That way settings/rules inside user.ini are applied to parts which they are not made for.
If you only have one webspace, you better put every webapplication in a subdirectory.
webroot
-limesurvey
-joomla
In every subdirectory settings/rule can be applied via .user.ini/.htaccess etc.
I use different webspaces or subdomains to separate webapplications. That keeps the customization to a minimum.