01:45:48 PM Jul 22nd 2011
Did Fluttershy know Pinkie Pie was disguised in the hay bale? I'm under the impression she did because Rainbow Dash recognized Pinkie instantly. We could assume everyone else knows what kind of disguises she wears. Also, when Fluttershy fled from her, she took the package with her.
08:42:09 AM Oct 14th 2011
It's hard to tell since she's as likely to run from a hay bale with comical nose/glasses staring at her than Pinkie Pie herself at that moment. Still, as you mentioned, Fluttershy was able to grab the package just before leaving, which implies that she at least considered whatever bumped into her to be after it. And really, who's the most likely to wear these glasses?