Bamboo Flooring Face Nailing Issues

I'm working on my last row in the house and having issues with face nailing strand bamboo boards. About half of them (throughout the house) are not going below the flooring surface(finish head sticks up ever so slightly). I am predrilling with a 3/32 bit and then using 2 inch 6d finishing nails as prescribed by the manufacturer. It almost feels like there is enough vibration in the boards that it is not allowing for the nail to be countersunk. I called the manufacturer and they recommended trim screws that have almost a finish nail type head. I have reservations about screwing anything into flooring but I will try it for the remainder of the install...any tips on what I can do to try to get these nails that are sitting on the surface below the surface? I have a solid Dewalt nail punch and I can swing a heavy a$$ hammer with some force but it's not working...
Thank you in advanced for any help!

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