My first instinct — on lines from the top of the response body being missing — would be a header problem. Does your error_log have anything to say about the issue?

I'm not sure if Apache::GzipChain is actually the culprit. The reason I say this is twofold; the Vary header is missing, and the main handler won’t even have registered itself called like that from telnet. The Vary header is a list of factors used in content negotiation: Apache::GzipChain should always add ‘Accept-Encoding’ to the Vary header if it’s listed in the output chain in the conf. As for running, it even won’t register itself with Apache::OutputChain unless ‘gzip’ is found in the Accept-Encoding header.

Here are a few suggestion to try (in no overly particular order):

• Check your error_log.
• Try with Apache::PassHTML instead of Apache::Registry as the last module in the chain, and point it at a static html document. This should tell you if Apache::GzipChain is working properly by itself. To test this easily with telnet, add PerlSetVar GzipForce On in that directory container (that var bypasses the normal negotiation). You should see the proper headers, including Content-Encoding, followed by a bunch of garbage (the gzipped output).
• Update to the current versions off all the modules in the chain; if possible.
• Out of curiosity, try running with PerlSetHeader Off
• Make sure your Apache::Registry scripts play by the proper header rules outlined here.
• Make sure you don’t make any calls to $r->http_send_header.

That’s about all I can think of (I haven’t actually used Apache::OutputChain for quite a while, I’m an Apache::Filter user now ;). Hopefully one of those suggestion works, or at least leads you in the proper direction.