That is actually a minor bug. They are not really gone, if you exit the game and come back in they will be back. The problem is that I load and cache the portal list the first time you enter the portal chamber (because it takes a long time to read the portal files). Unfortunately if you have not entered the portal chamber before you create the 'auto stairs portal', it does not load the list, it just adds that one portal. Then when you go back, you see only that one. However when you leave the game and re-enter, it loads the complete list.