If the problem can be solved by disabling TCP windows scaling as OP mentioned in
http://daemonforums.org/showpost.php?p=3420&postcount=3 the problem is either caused by ipf or an intermediate router/firewall not understand this scaling mechanism.
Microsoft Vista has this scaling mechanism enabled by default. That is why many people experience these kind of problems only after the launch of Vista.
For some details about TCP window scaling, see
http://en.wikipedia.org/wiki/TCP_window_scale_option