In the events of Amazing Spider-Man #Brand New Day and after it becomes clear, that Peter somehow erased the knowledge of his secret identity from literally everyone. Neither villains nor heroes know who Spider-Man is anymore. In #590 Johnny Storm realizes he used to know Spider-Man's identity, but can't remember that. Spidey later (#591) explains to Reed how this all works.
However, MJ still knows his identity. There's a hint in #559-561, where she talks to him over PA and says that they met in another life.
Later in #601, when Peter and MJ agree to meet, but she oversleeps and misses it, she watches news about Spidey and knows it's Peter.
If everyone's mind has been swept off, as Peter points and explains to Reed, how come that MJ still knows who Spider-Man is?
As per @Shreedhar comment, this clearly implies MJ thinks that Peter talks himself up by talking Spidey up.
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