I'm having the same exact issue after just mounting my backplate down and screw in the thumb screws until completely tightened. I may be using the same board and maybe too thin?
Please let me know what u did as now I'm stuck middle of build.
What I can do and use 2 black washers in kit not used and put them above board to compress the screw into. The plate will tighten to board then. I have yet to put the pump on to see if contact will be made to CPU but still looks like it will.
I'm using 399 msi godlike mb and 9900k