You have a point there, about Lenalee not reacting normally sometimes. We'll never really know the full extent of what the Order did to her until Hoshino tells us, but like you said, it was probably bad enough to cause her to lose something emotionally. Maybe she's still in the recovery process, since Cross did say she expresses herself better compared to her past self.
She'll probably get better once she's able to straighten out her emotions, if ever.