Hi Mic,
Glad you got the email from your boss!
A lot changed between 5.3 and 6.1, so it's not surprising to see some changes. I really cannot think of a change that would affect your output like this, but obviously something happened. So why this is happening depends on a few things:
What doctype is being used?
What stylesheet is being used?
Are any customizations or third party utilities involved?
Unfortunately, either way it looks like you may need to go to the government, and ask if they have an updated version of the stylesheet, but we'll try to provide any feedback or evidence you can show them to move the process forward.