On Linux Mint 12 "Lisa" 32-bit Firefox 11 respects the setting "Use system proxy settings".Details:
Used Mint system: Linux Mint 12 "Lisa", 32-bit, running among other things Firefox 11, version 11.0+build1-0ubuntu0.11.10.1. The repository where I got it from may have been http://ppa.launchpad.net/ubuntu-mozilla ... ppa/ubuntu
This system has been backed up and turnt into a usable live system with the help of Remastersys v2.0.18-1.
This live system was booted up on my normal office notebook.
Next the required company proxy settings were configured: Network Manager => Network Settings => Proxy Settings => Manual. The proxy server and proxy port were entered for http, https, ftp and socks. Then the button [apply systemwide] was pressed.
Next Firefox 11 was launched and it was configured like this: Edit => Preferences => Advanced => Network => Connections => Settings. Select the 3rd option from the top: (*) Use system proxy settings.
Have been using Firefox 11 on this live system now for more than an hour now. Have visited internal webpages (bypassing the proxy) as well as external webpages (requiring the proxy connection). Have not experienced any trouble so far.
As a matter of fact, I am writing this reply inside this same Firefox, running inside the Mint 12 live system.Conclusion:
Firefox 11 on Linux does not exhibit a general problem in using a systemwide proxy when told to do so. This does not explain why you experience such a problem. It should not be caused by a Firefox 11 bug.