The Navy, for one, had not updated their DMM for nearly a decade and were working with old rules.
In fact, they didn't even have the regulatory updates that implemented Motor Voter (which occupies a nice chunk of the DMM if you kind of wondered who is in charge of it).
The State of Florida still relied on postmarks although federal law had changed to provide for free mailing for certain ballot materials (including military absentee ballots). Since Congress can pass and enforce laws concerning federal elections ~ to wit, President, VP, Senate, House ~ and they made those items free, other federal law, to wit, USPS Domestic Mail Manual, superceded the force and effect of the Florida law.
It was up to Florida to fix their law, not for the Navy to begin postmarking anything. If Navy is now postmarking stuff, good for them. Taking a quick look through the DMM I still don't see any changes that require postmarking postage free mail. Do you?
During the 2004 election, I saw a piece on Fox News where they were aboard a Navy ship, and showed footage of a voting area set up and the on board post office actually running the ballots through a post marking machine. They wanted no doubts that the military ballots were date stamped by election day. I know what I saw. I will research further however and get back to you, if you still have doubts.