Is the GPU time spiking when not running the debugger? Basically are you 
getting like 99% of your frames hitting your frame, then 1% that are taking 4-5 
times longer than they are supposed to. 

I suspect you may have some kind of threading issue. Its easy to see slightly 
changing the timing of a few calls can put things into conflict over sharing a 
resource where as before they where not. Seeing if you have a continues load 
difference versus one with high peaks may help this. 

Improving batching may help if the conflicts are on the driver side of things...

On a somewhat related issue I ran into an a while back where the windows system 
call:

::timeBeginPeriod

was used. This caused the Nvidia driver to dead-lock, with large periodic 
hangs, and from time to time, just plane crashing.

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