What does the constitutional prohibition against ex post facto laws mean?

An ex post facto law is one that prohibits that which was formerly legal, and reaches back in time to punish that which was already done back when it was legal. It also includes retroactively increasing the punishment for past crimes. The US Constitution, Art 1, sec 9, prohibits such laws.

However, there is a great deal of legal controversy over whether a legal provision "punishes" the past act, and whether it is doing so retroactively. For example, suppose a state prohibits drunk driving as a misdemeanor, and you are convicted of it twice. Then the state passes a law making a third drunk driving offense a felony. Then you get caught drunk driving again. The state can punish you as a third drunk driver because the only thing that is being punished is your third act of drunk driving while having two priors, and your third act occurred after the law was passed.

In Kansas v Hendrick, 521 US 346 (1997), Hendricks was convicted of a sex offense in 1984 and sentenced. While in prison in 1994, Kansas passed a law for civil commitment of "sexually violent predators." After Hendricks served his criminal sentence, he was locked up anyway (though this time in a state hospital), with his acts leading to conviction and other past acts being the basis for a finding that he continued to be dangerous to the public, allowing his continued incarceration. The US Supreme Court, by a 5-4 vote, ruled that this "civil commitment" was not "punishment" and therefore allowed it to happen.

This ruling, in the eyes of many commentators, has gutted the ex post facto protection enshrined in the constitution.