I ran into this one. Basically the apt-cacher in the Jaunty repository (1.6.4ubuntu4) throws some error messages - "Error reading from server - read (104 Connection reset by peer)" - for some item checks requested by clients. It's fixed in upstream Debian Squeeze (ver 1.6.9) as far as I can tell. I had to download .deb directly from Debian, then used "apt-get -f install" to fix some dependency issues to dpkg it.
Another interesting issue I found is that the parser for /etc/apt/apt.conf.d/01proxy file in apt-get apparently ignores the proxy address, if you forget a semicolon in the header - I did precisely that, so having Acquire::http:Proxy in there - then it just silently went out without using proxy. It drove me nuts since there's no error message, until I paid close attention to my typing. :)
UPDATE: Now I ran into another bug, which prevents me from upgrading machines to Lucid. So I had to remove Debian apt-cacher (even their newest 1.6.11 doesn't work), and put on 1.6.7ubuntu4, which still has the original bug. Lesser of the two evils. Why can't Ubuntu and Debian address both?