I'm afraid I only saw a highlights package of his game against Gonzalez, so I can't give a complete opinion, but I didn't think he was moving at his best in that either.
But I watched the match in it's entirety today, and I'm absolutely positive he wasn't anywhere near his best physically. He was so late to the ball so often, and he couldn't seem to generate any real power, which even the most ardent of Nadal haters would admit is one of his strengths.
I would say the fact he got treatment in one game, lost the next, and had pulled out of Davis Cup prior to the loss for the same injury was a pretty good indication that he has a problem. How big a problem is debatable, but he looked nowhere near to his best today, IMO. How the match would have gone with both players playing at the level Del Potro was at (given Nadal is clearly capable of that) is anyone's guess.