Originally Posted by Chiaroscuro:
“I thought she did recognise him straight away with her greeting of "Hello sweetie". I must've misunderstood.”
Thinking back on that actually I think you're right. I think she was just teasing the Doctor, or thinking he was teasing her, until she confronted him. I don't think she can see through the Doctor's regenerations its just that she expected to see the Doctor there, having sent him a message on the psychic paper and knowing that no-one had set foot in the library for a century and the doctor stating he was a time traveller confirmed her suspicions.
Either River Song has met or, more likely seeing as she had a diary of events, travelled with the doctor in several regenerations. Checking which events he had already experienced backs this up as if she had only travelled with one regeneration then he would have either witnessed those events or not (Maybe I'm reading too much into this part). I reckon she just initially thought that the doctor was between regenerations or had undergone one after they had last met as she obviously can't know what the Doctor has looked like in previous regenerations.