[web-root]/js/main.js and [web-root]/name/js/main.js. In this case, you need to rename or move to another folder all equal files like [web-root]/js/main.js.The same issue can appear with folders. For example, if you have a page on website with URL “Contacts” (http://mywebsite.com/Contacts/) then the page will not work if you also have folder “Contacts” in website root folder.
2. If website is running on the Apache server then make sure that the Apache module “mod_rewrite” is enabled for website host. Without this module website may look completely messed up — with no images and styles loaded.
3. Please open file “.htaccess” located in web root folder of your website. Delete (or comment) all the content (if there is one) between lines “#### PERSISTENT CONTENT ####” and “#### PERSISTENT CONTENT END ####”. After that reload website in browser and check whether the problem has gone.
4. Make sure that you are looking at the same version in site builder website and published website — that is maybe you see “Desktop” version in builder and “Wide” version in published website. Try resizing browser window with published website to see how it is changed (if other modes are enabled in builder).