The problem is that synaptic runs as root and has no access to the users gconf
settings (where the gnome proxy is stored). This is really difficult to solve.
One option would be to save settings like the proxy configuration to a file (via
gconftool-2 --get /system/http_proxy/use_http_proxy) before becoming root and
load it again when sudo/gksudo/su/gksu was run. Pretty hackish though :/
Just a short explaination about the real problem:
The problem is that synaptic runs as root and has no access to the users gconf
settings (where the gnome proxy is stored). This is really difficult to solve.
One option would be to save settings like the proxy configuration to a file (via http_proxy/ use_http_ proxy) before becoming root and
gconftool-2 --get /system/
load it again when sudo/gksudo/su/gksu was run. Pretty hackish though :/