While it is very possible ballots can, and do, get delayed, I'm with RTFM on this one. Nothing personal Santahog but your sources lately are less than reliable/credible.
Military Postal Service has very clear rules about outgoing mail sitting anywhere. Things getting blown overboard does happen but being mistaken for ammo is stretching it a LOT.
Tom is correct, military absentee ballots are not federal but state/local ballots mailed just like everybody else's and are counted in the precinct selected as "home." I had the choice of voting in Alameda or San Diego county, since that is where I was stationed at the time, while on deployment.
BTW Military Times DID have a poll in the latest issue that 69% polled were voting for Romney, and 55% thought he would win. To bad.