Well, that dot indeed troubles me. because of it, the aggregated JS-file does not load and that may indeed very well be the reason you can't get everything working.
I you run Autoptimize without CDN, are all your links (for CSS, JS, images, ...) on the same domain (oursite.com or blog.oursite.com) or are there already differences between those? Does everything work in that case (autoptimize without CDN)? Specifically, what is the URL for the autoptimize JS file at the end if you have CDN turned off?