I have the same problem in X3, and also had it in X2, and possibly X1 (I can't recall for sure). The meter in simple instrument tracks is very flaky. When it shows that I'm clipping, I reduce the volume slightly, and it still surges into the red. Then I keep reducing the volume little by little, until the red goes away. At that point the volume is very low and nowhere near clipping. I've stopped relying on the meters, and use my ears instead.