As a test I eliminated all CC64 control messages except one -- left that one at value 10.    Unchecked "reset controllers to Zero".    With a few stops and starts, I could see the CPU begin to rise in the Performance Module.   Changed it to value 0, CPU went back to effectively 0.    

Depending on the synth, if you play a bunch of notes with non-zero sustain, it can cause CPU usage to build up because a new voice is used for every sustaining note. This is especially true of physical modeling synths like Pianotek, but you're using Kontakt, right? Can you replicate the problem with a different synth?

Maybe it is the Kontakt instrument.   I had thought it was a standard that CC64 less than 63 is equivalent to 0.
 
From another forum: 
"Cubase has a MIDI CC mapper/filter built in.

Are you using a pedal or a switch? CC64 should only have 2 values - ≤63 off, ≥64 on, which is a switch's job."
 

More advanced continuous pedals and keyboards are capable of generating all values of CC64, and properly programmed synths can respond to "half-pedaling" with variable damping like a real piano. Most synths are only capable of full sustain or no sustain, so they are programmed to treat anything less than 64 as OFF, and anything >= 64 as ON. This is a function of the synth programming, not the sequencer or the keyboard.