It was Columbia that had a crack in its heat shield and disintegrated upon reentry.
I think that this problem existed before then to some extent. There was a change in the material used for insulation at one point, I believe, as you note joevol. IIRC, the problem started after that change...but the change was apparently necessary (it could have been for environmental reasons, but I'm not sure). That may be BS, but I seem to recall reading that.
The reason that they are noted every time now is because we go through extensive checks of the heat shield while in space, something that we didn't do before. The problems are usually not a big deal and are repaired when the shuttle returns. Obviously, they can sometimes be a bigger deal, as it was with Columbia...so that is the reason for the extensive checks now.