Unsetting upstream proxy does not unset environment variables
Setting an upstream proxy sets the following environment variables:
http_proxy
ftp_proxy
https_proxy
If you unset the settings in the interface, the environment variables are left set (but /etc/clearos/upstream_proxy.conf and /etc/profile.d/proxy.sh are cleared). Perhaps /etc/profile.d/proxy.sh should not be deleted but changed to unset the variables.
There may be a bug in the old issue tracker which has not been transferred which says unsetting the upstream proxy requires a reboot to have the change accepted. This could be the cause.