I started a new Career game with the latest version, and got up to a FL-T200 engine...which has the same bug; when I attach it to a capsule, it disappears, and I can't attach anything underneath it. I also can't exit the VAB screen without exiting the entire game.
UPDATE: I did a full uninstall of KSP and loaded the latest version in full (which I had done before, but always over the previous version), and it works now. There might have been a mod that somehow managed to get passed from one previous install to another that was causing the problem.