Not too sure about the presidents in-between, but I do know that now it is a sign of respect. Both Bushes' did too, if I'm not mistaken. Maybe he didn't notice, maybe he was too caught in the moment, or maybe he just didn't know. I was around a bunch of veterans though at the time, and all said "What the fuck is up with that?" He's considered the highest in command, and is supposed to salute back.
I hope it was just one of the reasons above though, and that he purposefully didn't salute back.