The postfix mailsystem used by ispconfig is based on virtual domains, so the transpport for virtual delivery is defined by virtual_transport and not mailbox_transport. But if you set virtual_transport to groupware, you will disable the delivery trogh ispconfig.
If you want to use ispconfig plus your groupware, you should con´sider if its better to add some additional maildelivery rules to the /var/vmail/.mailfilter file. This is the global mailfilter file called for all mail deliveries and it should be possible to send all emails as copy to your groupware-deliverprog. The syntax of this file is "maildrop" syntax.