After searching on here for a solution to my problem, I found that other people was having the same issue. There wasn't an answer that worked for me. I have found a solution for me and maybe this solution would work for others.
The original .htaccess file:
Options -Indexes
DirectoryIndex index.php
<IfModule mod_rewrite.c>
RewriteEngine On
#RewriteBase /
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^.*$ index.php?qa-rewrite=$0&%{QUERY_STRING} [L]
</IfModule>
I have added the following to my .htaccess:
Options -Indexes
DirectoryIndex index.php
<IfModule mod_rewrite.c>
RewriteEngine On
# Uncomment the next line if needed, typically for subdirectory setups
RewriteBase /
# Remove double slashes in the URL
RewriteCond %{REQUEST_URI} ^(.)//(.)$
RewriteRule . %1/%2 [R=301,L]
# Check if the request is not a file or a directory
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Rewrite all other requests to index.php
RewriteRule ^(.*)$ index.php?qa-rewrite=$1&%{QUERY_STRING} [L,QSA]
</IfModule>
The only issue with this fix is that while in the admin area, Q2A still doesn't ok the first url structure option. I am not sure why, but at least I have fixed my issue. Maybe this fix will help others!