Pop-ups in Chrome Cause Mountain Lion to Switch Spaces
This is also an issue that I have, whether a pop-up occurs or I open a new window in Chrome it switches to a non Chrome space on my machine. I am using 10.8.3 Mountain Lion OSx and can repro on another machine on the same build.

This leads me to think it's simply a bug and we'll need to wait for a better workaround or a fix from Apple and/or Chrome.