Something to do with the DAW? May be a bug? Is there a huge amount of Automation going on during the areas where the volume is spiking during the render??? Could be a specific VSTi or VST that's farting during those spots where the volume spikes.
Have you tried messing with your Buffer Settings? Have you updated your Audio Card drivers recently?
If your setup worked fine before this tune starting giving you these specific volume related issues... try to figure out what's changed since your last tune (when there were no issues).