htaccess is not something specific to cPanel but apache that is behind several admin tool like cPanel, Plesk, ....
As you mentioned this is a potential problem with htaccess, I suggest that you have a look in the documentation of the author of the extension that provide you the SEF (acesef, sh404sef, ...)
If you are not using any additional extension to manage the SEF and only using the native Joomla SEF, you have to check again with rewritebase that is mentioned by Joomla as the parameter that must be potentially adapted.
Try to put it in comment and review again all the possible values.
If you have a slave site in the HTTP://....../joomla/slave1 and that
...../joomla is your master, perhaps you have to test a rewritebase like Rewritebase /joomla/slave1/