I just did floors 1-4 on c2 and even though the Guide Mode box was unchecked I still got a -5% penalty for it. I've even checked my map and there is nothing showing me the 'Critical Path' so I'm being penalized without getting any advantage. Does anyone know why this happening and what I can do to fix it?

You always get the guide mode penalty, unless you are in c6, I believe.

It's because in lower complexities, there are no bonus rooms, so you're always on the critical path.

Oh well, I guess I'll just have to deal with the penalty when I'm rushing lower floors. Thank you for the replies.