From research on the topic (I wrote a thesis paper about it), I found that the Vietnamese held POWs after the war as leverage, just as they held french POWs after the First Indochina War. They were referred to as "pearls." The Vietnamese would trade these "Pearls" for money, goods, almost anything. It was a way to recoup some of the expenses of fighting a war on their own land.
The problem after the Second Indochina War, was that the US government did not follow through on some of the promises made during the cease fire. I do not recall the specific number, but there was a significant number of millions of dollars that were promised to the Vietnamese government as part of the cease fire. Shortly after the agreement was made by President Nixon, President Ford took office, and refused to give the Vietnamese government anything. Thus, they refused to return the human collateral.
The other issue regarding POWs being kept after the war also involves a failure by the government at the time. The Pathet Lao, who were controlling Laos at the time, openly stated that they had US servicemen, and that they would not release them until the US government made a separate peace treaty with Laos. The US goverment refused, on the basis that there had never officially been a war with, in, around, or anywhere near Laos, and the servicemen in question were never seen or heard from again.
Sorry for the long post, but with my research, I feel I know about as much as one can without any operational knowledge. I will try to find some links, but I wasn't planning on cutting and pasting footnotes from my paper.