Improving segmentation diffusion
In your images, it seems regions are defined more by their edge boundaries rather than their colour. 

Since the IFT is using a colour difference metric then it doesn't see much difference between some foreground and background super pixels.

Instead of colour difference I would try a different metric based on boundary edge strength.   For example, the weight of the edge between two nodes is set to the average edge strength along their shared super pixel boundary. You might need to define a minimum boundary length though, such as 20 pixels, otherwise noise can effect this.

I've used this measurement before to combine segmentation regions and it works well. Interestingly, I was getting the segmentations using the IFT on a per pixel basis. This method you are applying looks interesting!

You could also combine the two measurements.