Wow... I thought I was the only one with this issue. I had that problem too and also switched to disc caching (basic mode). But I'm not using MU. Just WP 3.0.1.
Here is the history of my problem:
Recently I decided to uninstall AIOSEOP plugin since I wrote (found on the net here and there) some code for doing the job without it. So I did that (and manually removed some entries in my DB that AIOSEOP left there) and everything was fine except WordPress wouldn't place canonical link in the header of categories and home page (I use static page as my front page). I thought it's OK since I have safe redirection with trailing slash that WordPress takes care of it.
Then Google Webmaster Tools detected the home page and one category page that have identical meta descriptions and titles. Of course the ones with and without the trailing slash in the URL and without the canonical link in the header. After little bit of investigation I figured out that W3TC is doing this - preventing the trailing slash to be added in the URL.
I did so many things and finally switched to basic disk caching. However the problem is not ending there. Then W3TC wouldn't collect the garbage and the pages were cached forever. So I've set Browser caching of HTML with an option "cache with max-age" and that worked. So now W3TC is refreshing the pages at the time specified in "Browser Cache settings" (and if there is change in terms of new comments, posts etc.) but ignoring the time given in "Page Cache Settings". Actually I'm thinking that in basic disk caching mode, disk caching is not used at all. Now in my .htaccess file I have just the rules for "Browser caching" since I'm using the basic disk caching, and there is no .htaccess file in the directory /wp-content/w3tc/pgcache/ as with disc cache (enhanced).
The puzzle for me is: When the problem started? When the redirection stoped working? When I've unistalled AIOSEOP plugin or when I've upgraded to version 0.9.1.3 of W3TC which was very long time ago. It could be the second one and I didn't notice it because all the pages had canonical links in the header and there was no any duplicate content issue to be shown.
I'm thinking of three possible solutions/steps here.
1. Putting my back up online (AIOSEOP and W3TC installed, my code removed) and check out if redirection works or not. If the redirection is not working, then
1. Reverting to 0.9.1.2 version of W3TC. Many high traffic sites are not using the newest version like: mashable.com, makeuseof.com and yoast.com (Yoast and Frederick are actually friends and I think they're working together on some projects), or
2. Reinstalling the WordpRess and see what happens.
Sorry for the very long comment. Any ideas?