Is it possible to test with the VPN removed from the equation? IE connecting to the server directly via "open remote" or testing while on-site?
My imagination leans towards something in the network stack is not allowing the traffic required for uploading via the VPN to the server container is causing the crash. And a lack of graceful failing on that low level in filemaker causes it to hang and crash.
Also what OS is the server on, windows as well? I've gotten some strange container behavior before going cross-platform.
If you're unable to diagnose, it might be worthwhile to look into supercontainer or an FM12 upgrade, as both provide significant upgrades to the capabilities of the container field.