Not sure if it is the case for all, but just as a work around incase.
 – Create a text file with all the IPv6 addresses separated by new line
$ cat ipv6.txt
2001::1
2001::2
2001::3

write a one liner script to add them to interface.
#!/bin/bash
for ipv6 in `cat /etc/ipv6.txt`; do
/usr/local/directadmin/scripts/addip $ipv6 255.255.255.255 eth0
done

Add this as a post-up to /etc/network/interfaces

You may still need to add them from the direct admin interface so that you can manage them.

./arun