The first disconnect on the secondary side of a transformer is a seperately derived service, and the code says a service must have a grounded conductor. To achieve this in the situation you described you will have to ground one of the secondary phases. This is called corner grounding and it seems counter-intuitive the first time you do it. The conductor that is grounded must now be grey or white (although I usually put a band of the original phase color on the end as well) and then LABEL EVERYTHING because it's confusing for the next guy.
