I've honestly never seen that before, but by the picture you showed us, it's nothing to worry about. It looks like the hs is covering the entire procc, so it will dissipate the heat either way.
And your post is kind of confusing. If your temps arent getting better compared to stock, make sure you've got it seated correctly. Make a very thin even coat of thermal paste across the bottom of the heatsink, and make sure the clips are all tightly secured.
If it's still not working correctly after that, just RMA for a better cooler, or quit overclocking to to moon. :P