Why Samus is justified in freaking the hell out at Ridley in Other M, and other things:

-Every other time she fought Ridley before, it was the same Ridley.  The Ridley from Prime was the same Ridley from the first Metroid, just having to survive through cybernetic enhancements.  The Ridley from Super Metroid was the same one.  Ridley was supposed to be DEAD.  She thought she had finally won, finding her way out of her emotional torment.  Of course she's going to be shocked that suddenly he's alive again, and she hadn't discovered he was a clone at this point. In Fusion, while it is the same clone, it is just a virally reanimated version, and is not really the same being at all, therefore possibly not triggering the psychological issues due to internal rationalization.

-System limitations of previous games prevented them from displaying this type of emotion before.  You can't very well show Samus's shock/depression/anger at Ridley on a 16 bit system.  It's arguably harder to show in the Prime series, where it's in first person /and/ she doesn't talk at all. Not to mention Sakamoto, the creator of the franchise, disregarded the Prime games entirely for not being in his "vision" of the series (something he could have said earlier), meaning that while we might be able to look at the events of the game, the portrayal of Samus is wholly to be ignored there, for better or for worse.  I'm pretty sure if it weren't for these limitations, her PTSD would have been showcased a lot sooner. It was shown multiple times in the manga of the series, a version that shows the games in closer depth.

-PTSD can take many forms.  The severity of it can vary, as well as the emotions displayed when having a trauma attack.  In previous games, it might have been rage directed at Ridley, but in Other M it was shock because, again, she thought he was DEAD.  In fact, it's seen that she switches from shock to rage when Ridley presumably kills one of her best friends, Anthony Higgs. Not to mention that one of the symptoms of PTSD is emotional detachment, which shows in her voice more often than not in Other M. (The wikipedia article that cites straight from the Diagnostic and Statistical Manual of Mental Disorders, THE book on psychological issues: http://en.wikipedia.org/wiki/Posttraumatic_stress_disorder#Criteria)