(I'm currently running 4.5a (4.51.0.2048) )
We are testing a relatively new commercial web protection software system (Made by MXlogic, sold as McAfee SaaS Web Protection). This system runs 100% of all web traffic through one of several proxy servers worldwide. (It is able to handle a new class of malware that travels via "Web 2.0" back channels.)
To accomplish this, several different methods are available for manual or automated management of the Windows Proxy Server settings (in Ctrl Panel -> Internet Options -> Connections). This can be important because a variety of contexts can cause the proxy to change. For example, a person traveling with a laptop will need different settings in different regions of the world.
So far, all software I've tried keys off of the Windows Proxy settings, and automatically works correctly with the configured proxy server. Except one.
Logos 4 has its own separate proxy setting, and pays no attention to the configured setting.
I highly recommend changing this, so that Logos can function transparently for users who make use of proxy server settings.