I seem to be having the same problem: I've found no less than 7-8 Star Stones (and four bloodstones, one of which is used up) but the last room I've unlocked was the first Elemental Hall. After that, nothing. I thought at first that that was because I had to *pick up* Star Stones, but they seem to always go inert as soon as I approach them, but after reading this thread, it seems my error was that I did not visit the Homestead right away after finding each? But that would be extremely unpractical in some occasions, such as after the Star Stone in Immaculate Proving Grounds--if you teleport out immediately, you'd have to redo the entire dungeon!
Now my Homestead is under attack, and I can't open new rooms, anyway, but it would be nice to learn how to fix it for the future. :-/ Maybe there's some console command for that?