Stean, did you every come up with a solution to this? I am experiencing the same, and thought I had a solution but that turned out to be incorrect.
I'm experiencing the same behavior, QV11 seems to take the IE proxy settings while QV12 is not. I've tried to force the proxy settings in a number of ways with no luck. Appreciate any insight you might have.
Basically looks like this is due to a new library being used, and there is both a problem investigation (QV-11063) and enhancement request (QLIK-76679) around this. The following is from the article, although I'm not sure I completely follow:
Workaround until the bug fix: Proxy has to be configured in order to authenticate all communication for the url that is used for example http://maps.googleapis.com/maps/api/* so if it's possible, at proxy level, white-list all requests for the domain that is used.