I know that there was a pull request for this that was reverted for 1.6.4 but I think we should still look at fixing this. I just ran into this bug. Here is an example:
Does not work
maldet --background --scan-all '/var/www/vhosts/example.com/' --config-option email_addr=you@domain.com,quarantine_hits=1
Works
maldet --config-option email_addr=you@domain.com,quarantine_hits=1 --background --scan-all '/var/www/vhosts/example.com/'