Go to "CWP->Log Viewer" on the panel, select "error log" and then the domain that is causing you trouble, if you see something like this:
bla bla bla date, time whatever (.....) public_html/websites/.htaccess: Option FollowSymlinks not allowed here
Then do this:
Go to each single vHost file contained in "/usr/local/apache/conf.d/vhosts" and allow "FollowSymLinks", by adding it to the "AllowOverride" section, like in the following example:
<Directory "/home/-------------/public_html/websites">
Options -Indexes FollowSymLinks <-delete here
AllowOverride All Options=ExecCGI,Includes,IncludesNOEXEC,Indexes,MultiViews,SymLinksIfOwnerMatch,FollowSymLinks <-add here
</Directory>
Restart apache
And it will work
But try at first to do this to a domain that is not working for you, if it does the job do the same for all of them