Instead of cutting could you use the cropping tool in the "bitmap parameters" tab of your map in the material editor ?
Then you could just apply the atlas like a regular bitmap onto the native GrowFX leaf mesh.
I am not sure if this is exactly what you need, but it would allow you avoid using instances. I am not really sure if my method is the correct way, but it works for me.
Try rotating the pivot of your instance object. It looks like GrowFX deforms instances along the z axis. On a flat object there is no z info. You have to align the z to the long axis (the one you want to bend).
In the image on the original post it looks like the z is aligned to the long axis, unless the leaves were created flat and then rotated into position. This wouldn't change the pivot and would give the above result of a flat non conforming leaf.
also, make sure that you cut some segments in your geometry to allow for the bend.
Hope it helps !