Whoa! Firefox 48 opens the Windows proxy settings now! That is not good. I especially use Firefox so that in a corporate environment I can use different proxy settings than IE.
Was in the same corporate boat as you a while back. The FoxyProxy addon [1] is much more flexible, I recommend you switch to that since it enables quick toggling between the IE proxy and your configured ones.
FoxyProxy also lets you set different proxies for different pages. So you can run one proxy to be able to access the corporate intranet from outside, and another to access a non-public testing webpage, etc.
Just did a quick test with a clean profile and then I get the normal proxy window. I previously had several add-on installed to do some more advanced proxy settings, that probably bit me with the upgrade to Firefox 48.
