Looks to me as if you have been bitten by this bug: http://drupal.org/node/13148
After rereading it, I think you're right - I missed the part about proxy servers.
When I read that thread and I lost track or who was talking about which issue. Correct if I'm wrong but it seems there are two opposing desires. One is to maintain standards at the cost of SE rankings and visitors, while the other wants the world to see their website properly.
Someone in there also said this issue only affected the bots. I disagree. From my logs:
"Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1; .NET CLR 1.0.3705; .NET CLR 1.1.4322)" ac5-webproxy26.direcpc.com - - [06/Dec/2005:12:11:31 -0700] "GET /growing- vegetables/modules/event/event.js HTTP/1.0" 404 9595 "http://www.farm- garden.com/growing-vegetables/tomatoes" "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1; .NET CLR 1.0.3705; .NET CLR 1.1.4322)"
I believe that's a legitimate web browser coming through a DirecPC proxy server. They found the first page fine but messed up the second page. So to say this issue is strictly limited to bots which don't follow standards is incorrect.
I will discuss this with one of the Google engineers - if I can't get his attention long enough. ;)
Gregg