Is there a simple way to test a proxy to determine if it is correctly forwarding TCP and UDP traffic? An ideal method would be script-able.
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Your question may require more clarification, but it sounds like your concern is that the proxy may be stripping or modifying data. A proxy could combine fragments or something I guess, it would help if we knew the exact components you were working with.
However, in general if you want to test a difference in the packets "naturally" and through some type of proxy, you should capture traffic for the same action "naturally" and then through the proxy and do a comparison. You could capture traffic using Wireshark. Keep in mind you may only want to look at TCP/IP layer 5 data as the TCP specific things like the window and initial values should be different. In wireshark you can usually use one of the filters to compare the TCP stream data, and then you could just diff the natural and proxy captures.
In terms of doing this scriptable. You can using pcap or tcpdump and output it directly to a file. You would then need to write your logic to strip out everything but layer 5 and compare. There may be some scripts out there to just get the layer 5 stuff. Of course, if you are concerned about things at the lower layers as well, filter as needed.