First, the two cards become available when you beat Sora's game and save from the Battle Record ("End") screen. At that point, the game you just saved can be loaded and the second "special treasures" can be found in each world's Room of Rewards.
Second, beating Riku's game is NOT required. (Turns out the "clear bonus" banner is either a red herring or a poor implementation.)
Third, the clear saves needn't be found on the memory card as long as the KH:ReCoM System Data file is intact. (Keep them for backups, though.)
The referenced sections of my guide were corrected in v2.0. Look for the "flowchart" especially to help you pinpoint what went wrong.
Okay, to your question. If the Rewards room in, say, Twilight Town holds only one chest, then most likely you didn't save from Battle Record, or you're loading a different saved game (slim chance, but it's possible).
The only place where you might see only one chest with the correct saved game loaded is on 13F, where if the Rewards room was opened before facing the final boss, the room is still open afterward. Leaving the world and returning "fixes" that problem.
BTW, I've filed two more problem reports against the Cheats page, but they got filed, waiting for more reports to corroborate the info. If you have a moment, report ("have we been fooled?") any cheat that "doesn't work for me".