My first problem occurred when I moved my local site on localhost:8888/mywebsite to my server at http://www.mywebsite.com/tst. After moving the files and importing the database, in which I did a find and replace of the servername, I logged in to wp-admin and changed my cdn (s3) from static.dev.mywebsite.com to static.tst.mywebsite.com. After this I changed all the urls in the minify settings. I uploaded all my files to static.tst.mywebsite.com through the plugin, emptied all the caches en loaded my site in the browser. Everything was fine except my background images weren't there. In firebug I saw that in my minified css on static.tst.mywebsite.com all my background images urls were still pointing to /mywebsite/pathtoimage/image.jpg instead of to /tst/pathtoimage/image.jpg.
After trying a lot of things and rechecking everything twice I gave up and decided to start from scratch, which led me to my second problem.
So now I have a clean wp 3.0 install on my server, installed all my plugins and redid all my settings. After everything was ok I installed w3 total cache (development version again). After setting the writing permissions to wp-config and .htaccess all was good. Then I entered all my js and css urls in the minify settings and checked in the browser (love the preview mode btw). Still doing great so far. Now I activated the cdn setting and entered my bucket info. Then when I want to upload the minified files it says Total files: 0. Other files upload fine. And the css/js files aren't loaded in the browser. Strange thing is that when I try the url to a gzip minified file on the cdn I get an xml with access denied. Permissions problem somewhere?