Easy question, tough answer.
A pump is rated to output a certain amount of power, and it will do so, regardless of the flow restriction.
However...
Where you were using an Eheim 1048, resulting in a flow rate that allows the pump to be say, 70% efficient, you now have an Eheim 1250 which, although will give you a better flow rate, will also run with a flow rate that is much, much lower than its maximum output.
Look at it this way: if you used one of those 1.0 horsepower pool pumps, it would be struggling, right? Struggling to push more flow that is... It would certainly give you a better flow rate, but for the amount of power that this sucker is drawing, it's not very efficient at all.
But it still doesn't explain your results.
First, there's the additional pump heat that this beast will put in your rig, but the rad should be able to handle it.
The problem is that you're pushing your rad out of its sweet spot.
Try this: use the 1048 to loop the coolant through the rad, and the 1250 to loop the CPU waterblock. (yes, a dual res).
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