I think more than anything, he was surprised that Nalbandian turned up his game. He blew him off of the court in the 1st set and was holding easily in the 2nd until he was broken as you said. He was surprised that Nalbandian started serving really well and then before he knew it, he's in a third set with a guy who can't miss and brimming with confidence.
Would you compare this to the Dubai match against Nadal, then? I mean, Federer swept that first set and was holding with ease in the second set until the one crucial break. I haven't seen the match yet.
In any case, I like Nalbandian and am glad for him - I hope if they do meet in Basel, though, Federer can beat him, since it is his home tournament. I also hope Federer will play Paris this year since it's one of the three Masters Series events he hasn't won (and the other two are clay events)... of course, since they're changing the Masters Series system, maybe that won't be so important any more, but it'd be nice to have Federer win all of them someday.
I don't think the chances of his playing Paris is too strong, though, especially if he wins Basel.