As I understand it, the new 'experimental' backups setting uses gunzip and/or tar to create the archives rather than zip. I think most Linux systems come with 'tar' but maybe not 'gunzip'. Does your system have tar/gzip? Reason I ask is your statement about runs and executes in 2 seconds.
And the command line version uses the settings one has in
/admin/settings.php?section=backupgeneralsettings
Plus ... have you checked /admin/settings.php?section=automated
There are settings in there that would affect autobackups as well as the command line versions.
Keep 1, skip hidden, skip courses not modified in X days, automated backup storage I would set to 'specified directory for automated backups' and the destination to be outside of moodledata.
Also check into suPHP rules. It might be the culprit. Apache error logs show nothing?
'spirit of sharing', Ken
PS - now that there is a command line backup script, wonder if there will be a 'restore' script to compliment it. Hope so cause if Moodle is struggling with creating the backups it's likely (?) to struggle with restores via the Apache/Moodle UI.