So basically this is a custom/alternative mounting method? (Similar what I did with mine where I use the EVO212 clamp for the Thermalright Ultra Extreme).
The problem here (I THINK) is that it's possible that with this custom mounting method you can easily introduce stress, bending etc. eg. by over-tightening the screws etc...and the lack of a backplate doesn't help either, it would make the problem worse. The problem won't be apparent with the original "plastic clip" thingies because with them you are never able to introduce that big a force that it would bend anything as you can with the bolts.
So...as a first test you can try use the plastic clips again (because less pressure)..to see whether it also stresses the board and see whether it gives better temps.
Or..re-mount as you did before, but do NOT overtighten the screws at all, in fact try a very careful mount where the HSF sits "just right" but not more.
Other alternative...look for an option to mount (or an entire new cooler for that matter) with a backplate as well. EVO 212 is rather cheap. It's not "high end" but at least it could solve the problems with bending.
I would also recommend another method of applying TIM (not sure about Ceramique, anyone and their mama uses MX-4)..and then not spreading but a tiny blob or a tiny strip maybe 3/4 of an inch down the die like this:
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This MOBO has no such brace and the clamp warps the board when closed on the CPU.
If it's really that the CLAMP from the socket warps the board, something is off with the board. A backplate may also be the solution here, but I wouldn't say it's normal that closing the socket would warp the board, not at all.