About the last thing I can suggest would be to try and get a traffic capture for yourself using something like ComView or so and to see if you can pick up from that where the point of failure is. Or to revert it back to a standard setup (As closely as possible) and to try eliminating bit by bit.
Your setup is fairly unique in that it uses port 25 as it's main proxy port, is tunneling out of a corporate environment and into a home gateway who then provides internet access. (Is that a correct summation of it?)
One possibility is that there is a problem on the version of WinGate you are using. For example:
Release Notes wrote:5.2.2
3. Fixed the WWW proxy where downloads would occasionally be broken if scanning was disabled.
6.0
6. A major overhaul has been undertaken on the WWW Proxy. New features include:
- HTTP authentication by NTLM or HTTP Basic methods for proxy connections, TR intercepted connections, and server requests.
- Support for HTTP/1.1 including keep-alives and chunking (this results in a great improvement in performance) for proxy and server.
- Improved Support for server-parsed CGI (e.g. PHP) in readiness for our Webmail product.
With that in mind, you can use your 5.2 license key with 6.0. There is no upgrade required - you simply activate your earlier version's license key. It might pay to try that at some stage, to see if it could fix this problem for you.
If anything else springs to mind, I'll post back here.