It would have been more clear if the movie sequence showed Riku losing the Roxas the first time (when he was in a blindfold).

As for the scene with DiZ and cloaked Riku putting Roxas into the computer program... well it makes sense, doesn't it? Riku started concealing his entire face after he transformed into his dark form, Ansem. So presumably, he was beaten as blindfolded Riku, powered up as Ansem and wiped the floor with Roxas, then stuck an unconscious Roxas into the Twilight Town program with DiZ.