atopps

Here’s the full solution (until the next update) thanks to finglandj, as posted here (http://wordpress.org/support/topic/w3tc-is-discarding-directory-structure-when-using-cdn?replies=3)

The problem is occurring because of an erroneous replacement.

There is a script:

(function(){
				var srcStrt = "http://cdn10.brovadoweddings.com/blog/wp-content/uploads/p4/images/",
					bioData = [{"filename":"biopic1_1303345244.jpg","url":""},{"filename":"biopic2_1303345256.jpg","url":""},{"filename":"biopic3_1303345281.jpg","url":""},{"filename":"biopic4_1303345304.jpg","url":""}],
					picNum  = Math.floor(Math.random()*(bioData.length)),
					markup  = '<img id="biopic" src="'+srcStrt+bioData[picNum].filename+'" width="260" height="390" alt="MN Wedding Photography | Minneapolis Wedding Photographers | Engagement Photographer bio picture" class="bio-col" />';
				if ( bioData[picNum].url ) {
					markup = '<a href="'+bioData[picNum].url+'">'+markup+'</a>';
				}
				document.write(markup);
			})();

srcStart is getting modified by uri_to_cdn_uri which trims the trailing slash.

uri_to_cdn_uri is in w3-total-cache/lib/W3/Plugin/CdnCommon.php
Lines 544 and 550 trim slashes from the returned url. Changing those to an ltrim ensures the directory structure is maintained.