Because Congress was in recess for earlier Presidents, it wasn't when Obama made the appointments.
Congress alone gets to determine when it is in recess, but President Obama declared them in recess over a long weekend and made the appointments. That is what this case is about.
Normally, it is only when there is egregious abuse that the Supreme Court will agree to settle an argument between the other two branches. Even though a practice may not be in strict compliance with the constitution, the court will not step in unless one or the other goes too far. In this case, Oboma pushed beyond allowable limits, and the appeal court decided based on the constitution, not past practice. It is fairly clear that the original intent of the recess appointment power was to provide for continuity of government when the Senate was not physically available to consider appointments, not as a way to bypass the Senate when confirmation was unlikely or inconvenient. With a full time congress, recess appointments are actually no longer necessary and since the issue has been forced on them, the Supreme Court will likely rule that way.