If it didn't spike under boosted conditions with the stock cooler, it sure as hell shouldn't be doing it with the 212. Not a really great cooler, but it's a bit better than the Wraith coolers so if it didn't do that before, it shouldn't do it now.
Usually when a CPU spikes in temp under any kind of load conditions but is ok at idle, and I mean spikes beyond where it ought to be at for the conditions especially if we're not talking about running stress tests like Prime95, then it's because the installation wasn't done correctly. That is why I linked you to my article, because there is a specific reason why those coolers do that and that reason is defined in the guide. Almost everybody who installs the Hyper 212 EVO for the first time makes the mistake because they are not aware of it. That, or too much or too little thermal interface material is used, or the cooler bracket to backplate fasteners aren't done correctly. Something.
There is nothing about "software" that should have anything to do with a CPU spiking temps beyond specs under moderate loads, and gaming and most applications, even fairly strenuous ones, are moderate loads. Prime95, Heavyload, and other stress tests, those are substantial full loads.
What temperature are the CPU cores sitting at at idle with nothing open and just sitting on the desktop idle for like ten minutes?
What temperature is the CPU cores spiking to when you run something demanding?
What is the ambient temperature in the room where the unit is at?
And for what it's worth, the addition of practically ANY model of graphics card shouldn't have any kind of substantial impact on CPU core temps, especially not peak temps. It might raise the baseline a little bit, but if you had adequate case cooling it really shouldn't be any kind of factor at all. If the graphics card is adding that much heat to the internal case temps, then you need to figure out what is need to improve the case airflow. More fans, better fans, change the direction of airflow if it is not configured properly and by properly I mean all front, bottom and side fans should be configured as INTAKE fans, bringing cool air IN to the case, and all top or rear fans should be exhaust, taking air OUT of the case.