Actually the PHP setup is OK, as it allows full access to subdirectories of httpdocs, which is your site's root. JoomlaPack tries to find out if the parent of the site's root is a folder and fails due to open_basedir restrictions. This is a minor importance bug I'll just squash out (it just slipped through).
As a workaround, you can use the Javascript Redirects mode from the JoomlaPack Configuration page. As stated in the manual, it affects not only the backup process but the filter setup pages as well. So, instead of using AJAX in the directory exclusion page (which fails due to the bug) it'll use a more conservative method which will work.
Alternatively, you must set the "Error Reporting" to "None" from the Joomla! Global Configuration page (it's in the Server tab). In fact, this is the suggested setting for live sites and we consider this a "must be set" setting before attempting to backup, as stated in the manual.
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