System proxy settings inaccessible by Java, Firefox, VMware Fusion, etc.?
I have the same issue. When I use a proxy.pac file certain applications fail to pick up the settings. Among these are:


Firefox
Chrome
Java apps (like eclipse)


Some apps that do work with the pac file are:


Safari
Skype
Adium
Evernote


What I have found though, is that when I manually add a proxy server to the system preferences it is picked up by all applications. So something in the pac handling is broken. Maybe old/new APIs in Lion?