Can you make a SONAR project using Kontakt and OTS Stratosphere that shows this huge spiking?  I have OTS Stratosphere and I added a couple of instances and loaded those presets you mentioned and fed it some reasonable guitar MIDI files.  Inside Kontakt it was reporting the CPU around 20-25% but nothing crazy.  In Kontakt you can switch the instrument to info mode to see how many voices it's using and how much memory.  Might be a clue there.  Or if you can create a project that reproduces it reliably we could look at it.
 

For what it's worth, I've seen similar behaviour when untidy MIDI data was being sent to a Kontakt instrument.
 
In one case, there were a number of duplicate note events sent to a guitar instrument. In another case, there were a lot of zero-duration note events sent to a drum instrument (probably caused by some badly misjudged global MIDI edit operation). In both cases it appeared as if some Note Off events were not properly matched by the instrument which caused a small amount of CPU being wasted for each pending event even after the playback was stopped.
 
A couple of odd MIDI events didn't really matter, but when I kept repeatedly playing back the project, the tiny effect gradually cumulated until glitches, audio engine dropouts and even SONAR crashes started.

So it might be worthwhile to also take a look at the MIDI data stream that's being sent to the instrument.

filtersweep
Is it possible that there is some parameter in Stratos that I have mistakenly changed or perhaps a bug that causes this behaviour? I would be very interested to know if others can reproduce this problem or if others can run multiple jnstances of Stratos all day with no issues??

Try disabling Resonance in the Setup tab, I've found that to be a cpu spiker in any library that has Resonance turned on.