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Only one thing left to check: the FTP directory. As mentioned in the documentation:

Initial Directory. The FTP directory to your backup output directory. This path usually must be given in UNIX format, using forward slashes as path separators. If in doubt, use a graphical FTP client (i.e. FileZilla) to navigate to your backup output directory and copy the path displayed there to this field. For example, if your site's root is accessible in the httpdocs FTP directory and you use the default Akeeba Backup/JoomlaPack backup output directory (administrator/components/com_akeeba/backup and administrator/components/com_joomlapack/backup respectively) then you should enter httpdocs/administrator/components/com_akeeba/backup (or httpdocs/administrator/components/com_joomlapack/backup respectively) on this field.

That error means that you are still using the wrong FTP directory. Use Filezilla to connect to your site. Navigate into your backup output directory. Then, copy the path shown above the right-hand folder tree and paste it to ARC's FTP directory textbox. Save and take a new backup.

No, the .htaccess does not control the FTP access, only the web access. It's necessary to have this .htaccess file so that no unauthorized user can download the backup archives over the web.

I still think that the problem is the FTP path. Please send me a Personal message (I am user nicholas) with the following information:
1. URL to your site
2. Super Administrator username/password
3. FTP connection details (host, username, password)

I will test that locally and reply to your PM with the necessary settings to make Remote Control work with your site.