I had been fighting with this issue for several hours. Changing something in a script could make Visual Studio hang itself. It would use 100% of one of my CPU cores (using 25% of my CPU on a 4 core PC). This didn't only happen when saving a file in a script it also happened when changing the bundlerconfig.json file. I would have to restart Visual Studio, but this would just continue. It wouldn't crash it would just stand still and be unresponsive.
In order to fix this I changed the OutPutFileName in my bundlerconfig.json file. I had chosen Scripts/main.min.js as my output file. I changed this to Scripts/main.js (removing the min part) and voila! No more stalling of Visual Studio. In my solution I had a main.min.js file but no main.js file. I am not sure why this caused the issue.
Knowing that Mads Kristensen's work is top notch I believed for a long time, that it was something to do with my setup. I have used Web Essentials almost since it came out. This is the first time I have had a problem (Minifier and bundler was split from this extension).