Yes, Roundcube uses IMAP. As stated by Arieh, it connects to localhost:143.
Try enable debugging in /var/www/html/roundcubemail/config/main.inc.php and see logs:
// Log IMAP conversation to <log_dir>/imap or to syslog $rcmail_config['imap_debug'] = true;
Do you mean the .htaccess file reappears when updating? If so, then the problem is to have a different master .htaccess file, or to prevent it from being created.Same problem here. Renaming the .htaccess file works, but every update the problem will reoccur. Anybody who has an idee what's going on?