I was a middle child, and did the same sort of stuff. A lot of it was because I felt neglected because I had two younger siblings and didn't realize they needed more attention than I did (but wasn't old enough to understand at the time). I don't know what her room is like, but it was never "punishment" for me to get sent to my room because I didn't want to be around anybody anyway.
A few things:
Don't let her fool you: She knows exactly what she's doing, and she does it because she gets away with it. The crying and claiming she didn't know it was wrong is an act, plain and simple.
My parents would not have tolerated any of that behavior. As Bill Cosby said in "Bill Cosby: Himself", "Don't you roll your eyes at me; I'll knock them right out of your head!" As Dr. Phil says, kids need to be able to predict with 100% accuracy the consequences of their actions. Rolling the eyes and mouthing stuff is disrespectful to you (or whoever she does it to), and the attitude can no longer be tolerated. If there are consequences EVERY time it happens, then she'll eventually reconsider the behavior if she KNOWS that you're going to follow through.
She needs to realize there are consequences to her actions. If she chooses the behavior (rolling the eyes, mouthing words, having extra air in her mouth, etc, which is all disrespectful), she chooses the consequence. If you're going to "put her in time out" (which is basically what's going on), then make it a real time out in an appropriately designated spot (out in the open, like in a corner, or on a step or on a bench in a corner) for 6 minutes (1 minute per year of age).
If you don't want to go that route, you can start giving her extra duties around the house like clearing the table or taking the trash out. If those chores are assigned to her brother, then he gets a "free pass" because he was behaving and not acting like that.
The last thing I'd like to suggest would be to set aside "special time" for her. Find an activity you two can do together; or let her decide what's going to be for dinner on Monday nights, and let her help. Something/anything to make her feel special. Sometimes the "middle kids" don't get as much attention because hte younger child is getting potty trained and the older child has some school related activity (sport's practice?) and then what's she got? Tuesday night is our night to take our 6 year old to gym class. We go to Wendy's for dinner, then to gym class, and she loves it. Maybe she could do something like that, or take ballet/tap classes?
Just some thoughts for what it's worth - good luck!