Global_Hi_Flyer, I've had the same thing happen in ORD. I was actually STANDING in the security line (which was pretty long) and had taken out my laptop, freedom baggie, etc so as to be ready to go when it came my turn - SOP for me. Idiot TSO who had nothing better to do than stand at the front of the security line and harass people came by about three times and told me to put my stuff away so that it was 2 bags. I told him every time that it didn't make any sense and that I'd have to pull it out again a few feet later. Finally I got the 'do you want to fly today?' line and, since I didn't really have the time or have any particular interest in dealing with this idiot, I stuffed it all back in and got my kicks glaring at him.

In other places I have had three carry-ons (rollaboard, laptop case, small purse) and I've been able to halfway stuff my purse into my laptop case to get past the gate agent... even with 75% of it still sticking out. Weirdly I've never been stopped doing that. So theoretically, you could do something similar by wedging part of your laptop case into your rollaboard or something similar.