I'm running jboss3.2.5/tomcat5.0.26 on linux 2.6.9-1.667, with default configurations. When clients request web pages (static HTML) normally (without being behind a proxy), there's no problem. If the request is made over VPN, it times out. I have tried with small files (<1.2kb) and very simple HTML (no CSS or JS links) and that works fine. However, anything bigger (like 2kb gif) times out at the client side. I have tried the same versions on Windows XP Pro and there's no problem. The VPN client can access other websites without any problems.
Figured it out: MTU value was too large.