I see what you mean. Besides some of the sidebar going poof, I can't even see anything in the footer..in IE6 that is.. =/
I'm not sure if it's maybe a <div> or closing </div> problem or not...but, when you checked it with the W3C Validator site...did you use the: Show Source and Verbose Output options?
Here's the link to it, using those two options. You should really care about the 49 errors though, because one of the 49 might be the culprit of why the sidebar isn't showing. ;)
When you get to that link I gave above, click on the "blue number" link, beside the word: Line, it will take you down the "source" of the page, right to where the "errors" are at.
Then fix them all accordingly..in your theme's files, or maybe even within your Posts. Hopefully after fixing the errors, the sidebar will come back again in IE6. If it doesn't, then report back here again lol..
spencerp
P.S. I really hate IE6, I just wish Microshit would stop using it and providing it. Just redirect everyone from their IE6 downloads page to the Firefox download page LoL!!